Lncrna-Mediated Regulation of SOX9 Expression in Basal Sub-Type 2 Breast Cancer Cells

Total Page:16

File Type:pdf, Size:1020Kb

Lncrna-Mediated Regulation of SOX9 Expression in Basal Sub-Type 2 Breast Cancer Cells Downloaded from rnajournal.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press 1 LncRNA-mediated regulation of SOX9 expression in basal sub-type 2 breast cancer cells 3 4 Aamira Tariq1,2*, Qinyu Hao2, Qinyu Sun2, Deepak K. Singh2, Mahdieh Jadaliha2, Yang 5 Zhang3, Neha Chetlangia2, Jian Ma3, Sarah E. Holton4, Rohit Bhargava4, Ashish Lal5, Supriya 6 G. Prasanth2, Kannanganattu V. Prasanth2* 7 8 1Department of Biosciences, Comsats Institute of Information Technology, Islamabad, 9 Pakistan 10 11 2Department of Cell and Developmental Biology, Cancer Center at Illinois, University of 12 Illinois at Urbana-Champaign, Urbana, IL, USA. 13 14 3Computational Biology Department, School of Computer Science, Carnegie Mellon 15 University, Pittsburgh, PA, USA. 16 17 4Department of Bioengineering and Beckman Institute of Advanced Science and 18 Technology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, 19 IL, USA. 20 21 5Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, 22 National Cancer Institute, National Institutes of Health, Bethesda, MD, USA. 23 24 Running title: LncRNA promotes breast cancer cell proliferation. 25 26 Key words: Nuclear lncRNA, Basal-like subtype, TNBC, Regulation, Enhancer 27 28 * Corresponding authors Tariq et al 1 Downloaded from rnajournal.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press 29 Aamira Tariq 30 Department of Biosciences, Comsats Institute of Information Technology, Islamabad, 31 Pakistan; Department of Cell and Developmental Biology, Cancer Center at Illinois, 32 University of Illinois at Urbana-Champaign, Urbana, IL, USA 33 E.mail [email protected] 34 Kannanganattu V. Prasanth 35 Department of Cell and Developmental Biology, Cancer Center at Illinois, University of 36 Illinois at Urbana-Champaign, Urbana, IL, USA 37 E.mail [email protected] Tariq et al 2 Downloaded from rnajournal.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press 38 Abstract 39 40 Triple-negative breast cancer (TNBC) is one of the most aggressive breast cancer (BC) 41 subtypes with a poor prognosis and high recurrence rate. Recent studies have identified 42 vital roles played by several lncRNAs (long noncoding RNAs) in BC pathobiology. Cell type- 43 specific expression of lncRNAs and their potential role in regulating the expression of 44 oncogenic and tumor suppressor genes have made them promising cancer drug targets. By 45 performing a transcriptome screen in an isogenic TNBC/basal sub-type BC progression cell 46 line model, we recently reported ~1800 lncRNAs that display aberrant expression during 47 breast cancer progression. Mechanistic studies on one such nuclear-retained lncRNA, 48 linc02095, reveal that it promotes breast cancer proliferation by facilitating the expression 49 of oncogenic transcription factor, SOX9. Both linc02095 and SOX9 display co-regulated 50 expression in BC patients as well in basal sub-type BC cell lines. Knockdown of linc02095 51 results in decreased BC cell proliferation, whereas its overexpression promotes cells 52 proliferation. Linc02095-depleted cells display reduced expression of SOX9 concomitant 53 with reduced RNA polymerase II occupancy at the SOX9 gene body as well as defective SOX9 54 mRNA export, implying that linc02095 positively regulates SOX9 transcription and mRNA 55 export. Finally, we identify a positive feedback loop in BC cells that controls the expression 56 of both linc02095 and SOX9. Thus, our results unearth tumor-promoting activities of a 57 nuclear lncRNA linc02095 by facilitating the expression of key oncogenic transcription 58 factor in BC. 59 Tariq et al 3 Downloaded from rnajournal.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press 60 Introduction 61 62 Breast cancer (BC) is a frequently diagnosed malignancy and a leading cause of death 63 amongst women across the globe (Siegel, Miller, & Jemal, 2016). Breast cancer, like most 64 other epithelial tumors, is a heterogeneous disease with diverse subtypes (Nguyen & 65 Massagué, 2007). These subtypes differ from each other in clinical behavior, therapeutic 66 response profiles, and the presence or absence of receptors such as estrogen receptor (ER), 67 progesterone receptor (PR), and human epidermal growth factor 2 (HER2). Based on 68 expression of these receptors, breast cancer is classified into different categories: luminal A 69 (ER+, PR+, and HER2-), luminal B (ER+, PR+ and HER2+/-), HER2-positive (ER-, PR-and 70 HER2-) and triple negative breast cancer (ER-, PR- and HER2-) (Jadaliha et al., 71 2016;(Weigelt, Baehner, & Reis-Filho, 2010). 72 Triple negative breast cancer (TNBC) has been further classified into two distinct 73 molecular subtypes; basal-like and claudin-low, based on their unique gene expression 74 profiles (Jadaliha et al., 2016). There are no targeted therapies available for TNBC, and 75 patients are typically treated with chemotherapy. However, TNBC patients display poor 76 outcomes due to disease heterogeneity and chemotherapy resistance(Lv et al., 2016) . 77 Less than 2% of the human genome encodes proteins; ~75% of the human genome encodes 78 non-coding RNAs that are: transcripts with no apparent protein-coding potential, such as 79 microRNAs (miRNAs), piwi-interacting RNAs (piRNAs) and the least understood long non- 80 coding RNAs (lncRNAs) (Prensner & Chinnaiyan, 2011). In general, lncRNAs range in size 81 between ~200bp to 100kb (Derrien et al., 2012). Genome-wide transcriptome analysis 82 revealed that the human genome harbors >16000 lncRNA genes 83 (https://www.gencodegenes.org/human/stats.html) (Jalali, Gandhi, & Scaria, 2016). Tariq et al 4 Downloaded from rnajournal.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press 84 Mechanistic studies on a handful of them revealed that lncRNAs along with their interacting 85 protein partners contribute towards the regulation of diverse biological processes, 86 including cell proliferation (Prensner & Chinnaiyan, 2011; Schmitt & Chang, 2016; Ulitsky & 87 Bartel, 2013). They achieve this by modulating gene expression via different molecular 88 mechanisms such as chromatin modification, transcription, protein activity and localization, 89 and post-transcriptional gene regulation (Xu, Kong, Chen, Ping, & Pang, 2017). In the 90 context of BC, recent studies have identified several hundreds of lncRNAs as plausible 91 prognostic markers of BC (Van Grembergen et al., 2016). The aberrant expression of 92 lncRNAs like CCAT2 (Cai, He, & Zhang, 2015), MALAT1 (Jin, Lu, Lin, & Ma, 2016), H19 93 (Matouk et al., 2014), HOTAIR (Gupta et al., 2010) and ZFAS1 (Hansji et al., 2016) has been 94 associated with BC metastasis. Moreover, tissue type- and cell type-specific expression of 95 lncRNAs have made them promising candidates to address BC cancer cell heterogeneity 96 (Cabili et al., 2011). 97 In the present study, we investigated the potential role of a TNBC up-regulated lncRNA, 98 linc02095, in BC cell proliferation. We observed elevated expression of both linc02095 and 99 its neighboring protein-coding gene SOX9 in TNBC patient samples. Gain- and loss-of- 100 function experiments revealed that linc02095 promotes cell proliferation and BC 101 progression in vitro. Furthermore, we found that both linc02095 and SOX9 regulated the 102 expression of each other, and this co-regulation is required for enhanced tumorigenic 103 activities of BC cells. Taken together, our results imply that linc02095 could function as an 104 oncogenic lncRNA in breast cancer via its role in promoting the expression of oncogenic 105 and pro-metastatic transcription factor SOX9. 106 Results Tariq et al 5 Downloaded from rnajournal.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press 107 108 Linc02095 is up-regulated in TNBC BC cells and patient samples 109 Human breast carcinoma could progress via sequential genetic modifications of benign 110 hyperplasia of mammary duct epithelial cells into atypical ductal hyperplasia, to ductal 111 carcinoma in situ, to invasive tumor localized to the breast or lymph node, ultimately 112 metastasizing to distant organs (Santner et al., 2001). In order to understand the role of 113 lncRNAs during breast cancer progression, we utilized a well-established isogenic 114 mammary epithelial cell line-derived triple negative breast cancer (TNBC or basal-sub type) 115 progression model system. This model system consists of three isogenic cell lines (M1, M3 116 and M4), all of them originally derived from non-tumorigenic MCF10A mammary epithelial 117 cells. The cell line series consist of MCF10A (M1), tumorigenic but less metastatic 118 MCF10CA1h (M3) and highly tumorigenic and metastatic MCF10CA1a.c11 (M4) cells. M3 119 gives predominantly well-differentiated low-grade carcinomas in the xeno-graft models (Fu 120 et al., 2010; Imbalzano, Tatarkova, Imbalzano, & Nickerson, 2009; Kadota et al., 2009; 121 Kadota et al., 2010; McKeen Polizzotti et al., 2012; B. Tang et al., 2003). 122 We recently performed poly A+ deep RNA-seq (~160-250 million paired-end 123 reads/sample) of M1, M2, M3 & M4 cells that were grown as three-dimensional (3D) acinar 124 or organoid-like structures in Matrigel for 7-10 days (Jadaliha et al., 2018). By analyzing the 125 RNA-seq, >1800 lncRNAs were de-regulated at least 2-fold in tumorigenic M3 cells 126 compared to the non-tumorigenic M1 cells (Jadaliha et al., 2018). Several of lncRNAs that 127 showed altered
Recommended publications
  • 3D Interactions with the Growth Hormone Locus in Cellular Signalling and Cancer-Related Pathways
    64 4 Journal of Molecular L Jain et al. 3D interactions with the GH locus 64:4 209–222 Endocrinology RESEARCH 3D interactions with the growth hormone locus in cellular signalling and cancer-related pathways Lekha Jain, Tayaza Fadason, William Schierding, Mark H Vickers, Justin M O’Sullivan and Jo K Perry Liggins Institute, University of Auckland, Auckland, New Zealand Correspondence should be addressed to J K Perry or J M O’Sullivan: [email protected] or [email protected] Abstract Growth hormone (GH) is a peptide hormone predominantly produced by the anterior Key Words pituitary and is essential for normal growth and metabolism. The GH locus contains f growth hormone locus five evolutionarily related genes under the control of an upstream locus control region f GH1 that coordinates tissue-specific expression of these genes. Compromised GH signalling f genome and genetic variation in these genes has been implicated in various disorders including f chromosome capture cancer. We hypothesised that regulatory regions within the GH locus coordinate f cancer expression of a gene network that extends the impact of the GH locus control region. We used the CoDeS3D algorithm to analyse 529 common single nucleotide polymorphisms (SNPs) across the GH locus. This algorithm identifies colocalised Hi-C and eQTL associations to determine which SNPs are associated with a change in gene expression at loci that physically interact within the nucleus. One hundred and eighty-one common SNPs were identified that interacted with 292 eGenes across 48 different tissues. One hundred and forty-five eGenes were regulated intrans .
    [Show full text]
  • Genes Uniquely Expressed in Human Growth Plate Chondrocytes Uncover
    Li et al. BMC Genomics (2017) 18:983 DOI 10.1186/s12864-017-4378-y RESEARCHARTICLE Open Access Genes uniquely expressed in human growth plate chondrocytes uncover a distinct regulatory network Bing Li1, Karthika Balasubramanian1, Deborah Krakow2,3,4 and Daniel H. Cohn1,2* Abstract Background: Chondrogenesis is the earliest stage of skeletal development and is a highly dynamic process, integrating the activities and functions of transcription factors, cell signaling molecules and extracellular matrix proteins. The molecular mechanisms underlying chondrogenesis have been extensively studied and multiple key regulators of this process have been identified. However, a genome-wide overview of the gene regulatory network in chondrogenesis has not been achieved. Results: In this study, employing RNA sequencing, we identified 332 protein coding genes and 34 long non-coding RNA (lncRNA) genes that are highly selectively expressed in human fetal growth plate chondrocytes. Among the protein coding genes, 32 genes were associated with 62 distinct human skeletal disorders and 153 genes were associated with skeletal defects in knockout mice, confirming their essential roles in skeletal formation. These gene products formed a comprehensive physical interaction network and participated in multiple cellular processes regulating skeletal development. The data also revealed 34 transcription factors and 11,334 distal enhancers that were uniquely active in chondrocytes, functioning as transcriptional regulators for the cartilage-selective genes. Conclusions: Our findings revealed a complex gene regulatory network controlling skeletal development whereby transcription factors, enhancers and lncRNAs participate in chondrogenesis by transcriptional regulation of key genes. Additionally, the cartilage-selective genes represent candidate genes for unsolved human skeletal disorders.
    [Show full text]
  • Improved Detection of Gene Fusions by Applying Statistical Methods Reveals New Oncogenic RNA Cancer Drivers
    bioRxiv preprint doi: https://doi.org/10.1101/659078; this version posted June 3, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Improved detection of gene fusions by applying statistical methods reveals new oncogenic RNA cancer drivers Roozbeh Dehghannasiri1, Donald Eric Freeman1,2, Milos Jordanski3, Gillian L. Hsieh1, Ana Damljanovic4, Erik Lehnert4, Julia Salzman1,2,5* Author affiliation 1Department of Biochemistry, Stanford University, Stanford, CA 94305 2Department of Biomedical Data Science, Stanford University, Stanford, CA 94305 3Department of Computer Science, University of Belgrade, Belgrade, Serbia 4Seven Bridges Genomics, Cambridge, MA 02142 5Stanford Cancer Institute, Stanford, CA 94305 *Corresponding author [email protected] Short Abstract: The extent to which gene fusions function as drivers of cancer remains a critical open question. Current algorithms do not sufficiently identify false-positive fusions arising during library preparation, sequencing, and alignment. Here, we introduce a new algorithm, DEEPEST, that uses statistical modeling to minimize false-positives while increasing the sensitivity of fusion detection. In 9,946 tumor RNA-sequencing datasets from The Cancer Genome Atlas (TCGA) across 33 tumor types, DEEPEST identifies 31,007 fusions, 30% more than identified by other methods, while calling ten-fold fewer false-positive fusions in non-transformed human tissues. We leverage the increased precision of DEEPEST to discover new cancer biology. For example, 888 new candidate oncogenes are identified based on over-representation in DEEPEST-Fusion calls, and 1,078 previously unreported fusions involving long intergenic noncoding RNAs partners, demonstrating a previously unappreciated prevalence and potential for function.
    [Show full text]
  • Cisplatin Treatment of Testicular Cancer Patients Introduces Long-Term Changes in the Epigenome Cecilie Bucher-Johannessen1, Christian M
    Bucher-Johannessen et al. Clinical Epigenetics (2019) 11:179 https://doi.org/10.1186/s13148-019-0764-4 RESEARCH Open Access Cisplatin treatment of testicular cancer patients introduces long-term changes in the epigenome Cecilie Bucher-Johannessen1, Christian M. Page2,3, Trine B. Haugen4 , Marcin W. Wojewodzic1, Sophie D. Fosså1,5,6, Tom Grotmol1, Hege S. Haugnes7,8† and Trine B. Rounge1,9*† Abstract Background: Cisplatin-based chemotherapy (CBCT) is part of standard treatment of several cancers. In testicular cancer (TC) survivors, an increased risk of developing metabolic syndrome (MetS) is observed. In this epigenome- wide association study, we investigated if CBCT relates to epigenetic changes (DNA methylation) and if epigenetic changes render individuals susceptible for developing MetS later in life. We analyzed methylation profiles, using the MethylationEPIC BeadChip, in samples collected ~ 16 years after treatment from 279 Norwegian TC survivors with known MetS status. Among the CBCT treated (n = 176) and non-treated (n = 103), 61 and 34 developed MetS, respectively. We used two linear regression models to identify if (i) CBCT results in epigenetic changes and (ii) epigenetic changes play a role in development of MetS. Then we investigated if these changes in (i) and (ii) links to genes, functional networks, and pathways related to MetS symptoms. Results: We identified 35 sites that were differentially methylated when comparing CBCT treated and untreated TC survivors. The PTK6–RAS–MAPk pathway was significantly enriched with these sites and infers a gene network of 13 genes with CACNA1D (involved in insulin release) as a network hub. We found nominal MetS-associations and a functional gene network with ABCG1 and NCF2 as network hubs.
    [Show full text]
  • Decoding the Regulatory Landscape of Melanoma Reveals TEADS As Regulators of the Invasive Cell State
    ARTICLE Received 15 Sep 2014 | Accepted 16 Feb 2015 | Published 9 Apr 2015 DOI: 10.1038/ncomms7683 OPEN Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state Annelien Verfaillie1,*, Hana Imrichova1,*, Zeynep Kalender Atak1,*, Michael Dewaele2,3, Florian Rambow2,3, Gert Hulselmans1, Valerie Christiaens1, Dmitry Svetlichnyy1, Flavie Luciani2,3, Laura Van den Mooter3,4, Sofie Claerhout3,4, Mark Fiers3, Fabrice Journe5, Ghanem-Elias Ghanem5, Carl Herrmann6, Georg Halder3,4, Jean-Christophe Marine2,3 & Stein Aerts1 Transcriptional reprogramming of proliferative melanoma cells into a phenotypically distinct invasive cell subpopulation is a critical event at the origin of metastatic spreading. Here we generate transcriptome, open chromatin and histone modification maps of melanoma cultures; and integrate this data with existing transcriptome and DNA methylation profiles from tumour biopsies to gain insight into the mechanisms underlying this key reprogramming event. This shows thousands of genomic regulatory regions underlying the proliferative and invasive states, identifying SOX10/MITF and AP-1/TEAD as regulators, respectively. Knockdown of TEADs shows a previously unrecognized role in the invasive gene network and establishes a causative link between these transcription factors, cell invasion and sensitivity to MAPK inhibitors. Using regulatory landscapes and in silico analysis, we show that transcriptional reprogramming underlies the distinct cellular states present in melanoma. Furthermore, it reveals an essential role for the TEADs, linking it to clinically relevant mechanisms such as invasion and resistance. 1 Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium. 2 Laboratory for Molecular Cancer Biology, Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium.
    [Show full text]
  • Lncrna-Mediated Regulation of SOX9 Expression in Basal Subtype Breast Cancer Cells
    Downloaded from rnajournal.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press LncRNA-mediated regulation of SOX9 expression in basal subtype breast cancer cells AAMIRA TARIQ,1,2 QINYU HAO,2 QINYU SUN,2 DEEPAK K. SINGH,2 MAHDIEH JADALIHA,2 YANG ZHANG,3 NEHA CHETLANGIA,2 JIAN MA,3 SARAH E. HOLTON,4 ROHIT BHARGAVA,4 ASHISH LAL,5 SUPRIYA G. PRASANTH,2 and KANNANGANATTU V. PRASANTH2 1Department of Biosciences, Comsats Institute of Information Technology, Islamabad 45550, Pakistan 2Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA 3Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA 4Department of Bioengineering and Beckman Institute of Advanced Science and Technology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA 5Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA ABSTRACT Triple-negative breast cancer (TNBC) is one of the most aggressive breast cancer (BC) subtypes with a poor prognosis and high recurrence rate. Recent studies have identified vital roles played by several lncRNAs (long noncoding RNAs) in BC pathobiology. Cell type-specific expression of lncRNAs and their potential role in regulating the expression of oncogenic and tumor suppressor genes have made them promising cancer drug targets. By performing a transcriptome screen in an isogenic TNBC/basal subtype BC progression cell line model, we recently reported ∼1800 lncRNAs that display aberrant expression during breast cancer progression.
    [Show full text]