- PROJECT 3 Long non-coding RNAs (lncRNAs) represent a large and relatively understudied class of RNAs that have great potential to provide novel opportunities to influence gene regulation and cancer biology. The long-term goal of Project 3 is to identify lncRNAs that are over-expressed in breast cancer, define their role in the disease, and develop approaches to manipulate their expression in vivo to impact breast cancer progression. Here, a series of Aims are presented to determine the roles of Malat1 lncRNA, and several recently identified lncRNAs - Mammary Tumor Associated RNAs (MaTARs) - that are expressed in mouse models of luminal B and Her2/neu mammary cancer. We showed that Malat1 is over-expressed in mammary tumors and its genetic loss or knockdown results in differentiation of the primary tumor and a significant reduction in metastasis. Studies are proposed to identify the steps in metastasis that are dependent upon Malat1 and the critical regions of the RNA contributing to its function. Mouse models containing GFP- or bioluminescently-labeled breast tumor cells will be used to follow metastasis and in vivo antisense oligonucleotide (ASO) knockdown will provide a means to reveal the specific dependencies of Malat1 in the metastatic process. 3D tumor organoid cultures will be used to ascertain functional domains within Malat1 and to identify critical regions that are essential for tumorigenesis. The promoters of mammary tumor genes that are impacted upon Malat1 knockdown are enriched in Sox5 and Tcfcp2l1 binding sites. Studies are proposed to examine the role of these transcription factors, in conjunction with Malat1, to regulate the differentiation of primary tumors and the significant reduction in metastasis upon Malat1 knockdown. A series of studies are proposed to determine the function of 4 recently identified MaTARs that are expressed in a mammary tumor-specific manner. Chromatin Isolation by RNA Purification (ChIRP) coupled to deep sequencing or mass spectrometry will be used to identify interacting DNA sequences and proteins. To evaluate the potential of these MaTARs as therapeutic targets genetic knockout mouse models will be established and crossed with mammary tumor models to assess the impact on tumor initiation, progression and metastasis. RNA-seq will be performed on knockout and wild-type tumors to identify global gene expression changes upon MaTAR loss. The expression level and breast cancer sub-type specificity of human MaTAR orthologs has been examined and will be correlated with overall and relapse-free survival, and metastatic incidence, and appropriate candidates will be studied in patient-derived xenograft mouse models. Together, the proposed studies will define the role of several lncRNAs in breast cancer biology, and determine their potential as therapeutic targets to impact breast cancer progression.

Public Health Relevance

- PROJECT 3 Project 3 will characterize the role of several long non-coding RNAs in mammary cancer biology and the impact of their genetic knockout, antisense knockdown, or over-expression on cancer progression and metastasis. The insights gained from this study will significantly impact considerations of new therapeutic approaches to treat breast cancer.

National Institute of Health (NIH)
National Cancer Institute (NCI)
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Cold Spring Harbor Laboratory
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Li, Meng Amy; Amaral, Paulo P; Cheung, Priscilla et al. (2017) A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylation. Elife 6:
Diermeier, Sarah D; Spector, David L (2017) Antisense Oligonucleotide-mediated Knockdown in Mammary Tumor Organoids. Bio Protoc 7:
Pelossof, Raphael; Fairchild, Lauren; Huang, Chun-Hao et al. (2017) Prediction of potent shRNAs with a sequential classification algorithm. Nat Biotechnol 35:350-353
Roe, Jae-Seok; Hwang, Chang-Il; Somerville, Tim D D et al. (2017) Enhancer Reprogramming Promotes Pancreatic Cancer Metastasis. Cell 170:875-888.e20
Zhang, Bin; Mao, Yuntao S; Diermeier, Sarah D et al. (2017) Identification and Characterization of a Class of MALAT1-like Genomic Loci. Cell Rep 19:1723-1738
Mu, Ping; Zhang, Zeda; Benelli, Matteo et al. (2017) SOX2 promotes lineage plasticity and antiandrogen resistance in TP53- and RB1-deficient prostate cancer. Science 355:84-88
Anczuków, Olga; Krainer, Adrian R (2016) Splicing-factor alterations in cancers. RNA 22:1285-301
Baker, Leena; BeGora, Michael; Au Yeung, Faith et al. (2016) Scribble is required for pregnancy-induced alveologenesis in the adult mammary gland. J Cell Sci 129:2307-15
Tasdemir, Nilgun; Banito, Ana; Roe, Jae-Seok et al. (2016) BRD4 Connects Enhancer Remodeling to Senescence Immune Surveillance. Cancer Discov 6:612-29
Hossain, Manzar; Stillman, Bruce (2016) Opposing roles for DNA replication initiator proteins ORC1 and CDC6 in control of Cyclin E gene transcription. Elife 5:

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