title: LIN28A Modulates Splicing and Gene Expression Programs in Breast Cancer Cells.
abstract: LIN28 is an evolutionarily conserved RNA-binding protein with critical functions in developmental timing and cancer. However, the molecular mechanisms underlying LIN28's oncogenic properties are yet to be described. RNA-protein immunoprecipitation coupled with genome-wide sequencing (RIP-Seq) analysis revealed significant LIN28 binding within 843 mRNAs in breast cancer cells. Many of the LIN28-bound mRNAs are implicated in the regulation of RNA and cell metabolism. We identify heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), a protein with multiple roles in mRNA metabolism, as a LIN28-interacting partner. Subsequently, we used a custom computational method to identify differentially spliced gene isoforms in LIN28 and hnRNP A1 small interfering RNA (siRNA)-treated cells. The results reveal that these proteins regulate alternative splicing and steady-state mRNA expression of genes implicated in aspects of breast cancer biology. Notably, cells lacking LIN28 undergo significant isoform switching of the ENAH gene, resulting in a decrease in the expression of the ENAH exon 11a isoform. The expression of ENAH isoform 11a has been shown to be elevated in breast cancers that express HER2. Intriguingly, analysis of publicly available array data from the Cancer Genome Atlas (TCGA) reveals that LIN28 expression in the HER2 subtype is significantly different from that in other breast cancer subtypes. Collectively, our data suggest that LIN28 may regulate splicing and gene expression programs that drive breast cancer subtype phenotypes.
authors.affiliation: Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Yang
authors.affiliation: Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.
authors.forename: Brian D
authors.initials: BD
authors.lastname: Bennett
authors.affiliation: Research and Development, Illumina, Inc., Hayward, California, USA.
authors.forename: Shujun
authors.initials: S
authors.lastname: Luo
authors.affiliation: Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.
authors.forename: Kaoru
authors.initials: K
authors.lastname: Inoue
authors.affiliation: Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.
authors.forename: Sara A
authors.initials: SA
authors.lastname: Grimm
authors.affiliation: Research and Development, Illumina, Inc., Hayward, California, USA.
authors.forename: Gary P
authors.initials: GP
authors.lastname: Schroth
authors.affiliation: Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.
authors.forename: Pierre R
authors.initials: PR
authors.lastname: Bushel
authors.affiliation: Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA kinyamu@niehs.nih.gov archer1@niehs.nih.gov.
authors.forename: H Karimi
authors.initials: HK
authors.lastname: Kinyamu
authors.affiliation: Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA kinyamu@niehs.nih.gov archer1@niehs.nih.gov.
authors.forename: Trevor K
authors.initials: TK
authors.lastname: Archer
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D001483:Base Sequence; D001943:Breast Neoplasms / Q000145:classification* / Q000235:genetics; D045744:Cell Line, Tumor; D005260:Female; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D000076245:Heterogeneous Nuclear Ribonucleoprotein A1; D034481:Heterogeneous-Nuclear Ribonucleoprotein Group A-B / Q000378:metabolism*; D006801:Humans; D061986:MCF-7 Cells; D008324:Mammary Tumor Virus, Mouse / Q000235:genetics; D008840:Microfilament Proteins / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D020033:Protein Isoforms / Q000096:biosynthesis; D034622:RNA Interference; D034741:RNA, Small Interfering; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D020079:Terminal Repeat Sequences / Q000235:genetics
chemical_list: C511939:Enah protein, human; D000076245:Heterogeneous Nuclear Ribonucleoprotein A1; D034481:Heterogeneous-Nuclear Ribonucleoprotein Group A-B; C000619657:Hnrnpa1 protein, mouse; C516326:LIN28B protein, human; D008840:Microfilament Proteins; D020033:Protein Isoforms; D034741:RNA, Small Interfering; D016601:RNA-Binding Proteins; C000619656:hnRNPA1 protein, human