第一章：三陰性乳癌為侵襲性最強的一種乳癌亞型，其預後和五年生存期皆不理想。目前臨床針對三陰性乳癌的治療上，最主要的挫折為相較於其他乳癌亞型，病人在初步治療後在五年內易發生轉移。轉移後增生在遠端重要器官如肺、肝及骨頭往往是致命的，也是三陰性乳癌病人的末期徵象。本研究的目標為要找尋三陰性乳癌發展及轉移增生的機制以期能開發新穎的治療策略來更有效治療病人。我們發現在高度惡性具有肺轉移及淋巴結轉移能力的三陰性乳癌細胞中大量表現CD24。移除CD24表現能抑制腫瘤生長、減少淋巴轉移及遠端肺轉移，並且也觀察到腫瘤血管及淋巴管的數量顯著地減少。移除CD24表現也進一步提升三陰性乳癌細胞裡EGFR/Met的蛋白質不穩定性，主要透過溶小體蛋白降解路徑，進而損傷EGFR/Met所媒介的訊號傳遞路徑及其下游的血管淋巴管生長相關分子如血管內皮生長因子A及C。利用CD24單株抗體治療有肺轉移的小鼠可延長其生存期。臨床數據分析顯示，高表達CD24 與MET的三陰性人有著極差的預後。我們總結CD24可作為三陰性乳癌的治療標的，而搭配MET的基因組合可作為病人的預後指標。
第二章： 延續第一章的研究，第二章的研究主軸為開發治療性的CD24單株抗體。利用Expi293 哺乳動物細胞表達系統，我們生產並純化融合蛋白CD24小鼠Fc，其能與它的天然受體P-selectin結合也驗證其生物活性。我們也利用純化的融合蛋白CD24小鼠Fc進行小鼠免疫，進而得到產生CD24單株抗體的小鼠。我們成功從此批小鼠的脾臟B細胞建立融合瘤，並挑選出九株能分泌CD24單株抗體的融合瘤。抗體功能性分析顯示，CD24單株抗體能成功誘發受體內化，抗體也能經由內化作用進入細胞內，但不影響癌細胞生長。表面電漿共振分析顯示抗體的親合力達10-9 to 10-13 M，表明了我們自製的CD24單株抗體為極具潛力的抗體藥物複合體。接下來，我們將會測試單株抗體的抗腫瘤能力。在未來，
我們也會與國家衛生研究院生藥所徐祖安實驗室合作進行並利用次世代定序及編碼技術取得抗體關鍵序列。我們的目標為利用抗體工程製造人類化抗體，並測試抗體之抗腫脹效能在人類化小鼠模型的基礎上。期望日後成功開發的抗體能應用在三陰性乳癌病人及有高表達CD24分子的癌症病人上。
第三章：本論文的第三章主要探討長鏈非編碼核醣核酸(lncRNA)在乳癌轉移的角色。LncRNA為長度超過200核苷酸的非編碼核醣核酸轉錄子，近年發現參與在各式各樣的細胞機制和癌細胞轉移。本篇旨在找出新穎的lncRNA參與調控細胞爬行及侵襲。我們比較低轉移性231細胞及高轉移性IV2細胞的lncRNA表現，找出73個轉移相關的lncRNA，並利用線上腫瘤資料庫，比對出一個新穎的lncRNA 名為LOC550643。臨床數據分析顯示高表達LOC550643的病人其5年存活期較差，特別是在三陰性病人。功能性的分析顯示抑制LOC550643可減低細胞爬行、侵襲及非依賴嵌入細胞生長的能力。並且我們發現抑制LOC550643表現可減低乳癌細胞肺轉移能力。進一步分析顯示抑制LOC550643能造成癌細胞生長緩慢主要透過影響細胞週期。另外我們也發現抑制LOC550643能減弱TGF-β訊號路徑。總結，我們的結果表明LOC550643參與了乳癌的生長與轉移，將來有機會作為乳癌有用的分子標記及有潛力的治療標的。

Chapter I
Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype, with unfavorable prognosis and 5-year survival. The major setback of clinical treatment of TNBC patients is that they tend to develop metastasis more quickly within first five years after initial treatment as compared to patients with other molecular subtypes of breast cancer. Metastatic colonization at vital organs such as lung, liver and bone is lethal and is considered the terminal stage of not only TNBC patients but all cancer patients. The purpose of our study was to investigate the underlying mechanisms involved in TNBC progression and metastatic colonization and to develop novel therapeutic approaches to better treat patients with TNBC. In chapter I, we determined that CD24 expression was elevated in highly lung and lymph node metastatic TNBC cells. CD24 depletion inhibited primary tumor growth and lymph node and lung metastasis and reduced the number of blood and lymphatic vessels in the tumor microenvironment. CD24 knockdown impaired EGFR/Met-mediated signaling and reduced lymphangiogenesis- and angiogenesis-related molecules, including vascular endothelial growth factors A and C, by promoting EGFR and Met protein instability via the lysosomal degradation pathway. CD24 monoclonal antibody treatment reduced lung metastasis and prolonged the survival in a lung metastasis mouse model. Clinical analyses revealed that the CD24high/METhigh “double-positive” signature identified a subset of TNBC patients with worst outcomes. We conclude that CD24 could be a therapeutic target by itself and in combination with the Met expression could be a good prognostic biomarker for TNBC patients.
Chapter II
This part of Ph.D. thesis aims to translate the findings of Chapter I into the development of therapeutic CD24 monoclonal antibody as well as the diagnostic and prognostic tools for TNBC (1). Given that CD24 is a GPI-anchored membrane protein, which is known for its hydrophobic nature and, therefore, difficult to isolate and purify (2). Therefore, we collaborated with Dr. Hsu in the Institute of Biotechnology and Pharmaceutical Research at NHRI to develop the therapeutic CD24 MAb and to test the inhibitory effect of the candidate MAbs. We will determine the sequences of the candidate MAbs by Next Generation Sequencing (NGS) coupled with a barcoded sequencing pipeline. Our ultimate goal is to engineer the candidate mouse CD24 MAbs into humanized MAbs to test their anti-tumor efficacy in the humanized mouse model. The success of this translational study will produce the first targeted monoclonal antibody (MAb) therapy for not only the patients with TNBC but also very likely the cancer patients with high CD24 expression.
Using the Expi293 mammalian cell expression system, we generated and purified mouse Fc-tagged CD24 recombinant protein and tested it for the bioactivity to bind to its naturally-occurring ligand P-selectin. Mice were immunized with purified CD24 recombinant protein and showed a successful humoral response. The FACS analysis showed that the mouse with humoral response was able to generate CD24-specific antibodies. The hybridoma was established using mouse splenocytes and the mouse myeloma cells. For now, we generated nine hybridoma clones that are able to secrete CD24-specific antibodies at the high concentration. The functionalities of CD24 monoclonal antibodies (MAbs) were tested. We found that nine CD24 MAbs are able to induce receptor internalization but do not display the inhibitory effect on cell proliferation. Surface plasmon resonance analysis demonstrated that the binding affinity of CD24 MAbs is ranging from 10-9 to 10-13 M, suggesting that our CD24 MAbs could be used as the candidate antibody for the future development of antibody drug conjugate (ADC). The in vivo anti-tumor capability of these nine CD24 MAbs are tested underway.
Chapter III
Metastasis is the major cause of death for patients with breast cancer; therefore, identifying the molecular mechanisms that regulate metastasis and developing of useful therapeutic strategies are important tasks. Long non-coding RNAs (LncRNAs), which are noncoding transcripts with over 200 nucleotides in length, have recently emerged as important molecules in several cellular processes, including cancer metastasis. The objective of this study is to unravel the novel lncRNAs involved in the regulation of cell migration and invasion in breast cancer. Results: 73 metastasis-related lncRNA candidates were identified from comparing paired isogenic high and low human metastatic breast cancer lines and the expressions were verified in clinical tumor samples using The Cancer Genome Atlas (TCGA). Among them, a novel lncRNA, LOC550643, is highly expressed in breast cancer cells as well as in other types of cancer cells. Furthermore, high expression of LOC550643 is significantly correlated with poor prognosis of breast cancer patients, especially for triple negative breast cancer (TNBC) patients. Functional assay showed that LOC550643 was able to regulate several in vitro metastatic traits such as cell migration, cell invasion, and anchorage-independent growth. We demonstrated that depletion of LOC550643 could suppress lung metastatic potential of breast cancer cells in a tail vein injection mouse model. Our data also revealed that LOC550643 knockdown could significant suppress breast cancer cell growth via impairing cell cycle progression. Furthermore, our results also demonstrated that silencing of loc550643 expression led to cell invasion inhibition, possibly by suppressing TGFß signaling. Thus, we showed that LOC550643 participated in breast cancer metastasis and growth, which could serve as a useful molecular biomarker for cancer diagnosis and a potential therapeutic target for breast cancer.

Table of Contents
Chapter I: Identification of CD24 as an oncogenesis regulator and therapeutic target for triple negative breast cancer progress
Introduction………………………………………………………………………14
Materials and Methods
Cell culture…………………………………………………………………………17
Flow cytometry…………………………………………………………………….18
Western blotting………………………………………………………………………18
In vivo selection of lung-dormant breast cancer cells and highly metastatic cells…19
RNA extraction……………………………………………………………………….19
Reverse transcription polymerase chain reaction……………………………………19
Immunofluorescence staining……………………………………………………20
Confocal microscopy…………………………………………………………………20
Lentivirus preparation……………………………………………………………20
shRNA gene knockdown…………………………………………………………20
Protein degradation assay…………………………………………………………21
Transwell invasion assay……………………………………………………………..21
Transwell migration assay………………………………………………….……...21
Endothelial cell tube formation assay……………………………………………22 Time lapse imaging……………………………………………………………22
Antibodies and reagents…………………………………………………………….22
In vivo metastasis…………………………………………………………………….22
Histological analysis………………………………………………………………..23
In vivo lung targeting……………………………………………………….……….23
In vivo monoclonal antibody treatment……………………………………………….23
Orthotopic xenograft mouse model……………………………………………….24
Oligonucleotide transfection………………………………………………………….24
Immunohistochemistry (IHC) staining……………………………………………….24
Gene set enrichment analysis (GSEA)………………………………………………25
Clinical dataset analysis……………………………………………………………25
Clinical samples………………………………………………………………………26
Statistics……………………………………………………………………………27
Results……………………………………………………………………………27
Figures………………………………………………………………………………49
Tables…………………………………………………………………………………76
References……………………………………………………………………………80
Chapter 2: Generation of therapeutic CD24 monoclonal antibody
Introduction…………………………………………………………………………..85
Materials and Methods
Construction of CD24-mFc plasmid………………………………………………….86
Expression and purification of recombinant CD24-mFc protein……………………86
Validation of purified CD24-mFc fusion protein……………………………………87
Immunization of mice ……………………………………………………………….87
Flow cytometry analysis ……………………………………………………………88
Surface plasma resonance (SPR) assay…………………………………………….88
Results……………………………………………………………………………….90
Figures……………………………………………………………………………97
Tables………………………………………………………………………………108
Reference……………………………………………………………………..……109
Chapter 3: Identification of the oncogenic role of a novel LncRNA LOC550643 to promote triple negative breast cancer progression
Introduction………………………………………………………………………..111
Materials and Methods
Cell line………………………………………..……………………………………112
5' and 3' Rapid Amplification of cDNA End (RACE)………………………………113
Subcellular localization fractionation………………………………… …………..113
LncRNA- protein binding assays on the human proteome Microarrays…………114
Microarray analysis………………………………………………………..……....115
Pathway enrichment analysis…………………………………………….........….115
Western blotting……………………………………………………………...…….116
RNA immunoprecipitation (RIP) ………………………………………………..116
Candidate target genes of miRNA and luciferase activity assay……………………117
Animal model…………………………………………………………………..…117
Results……………………………………………………………………………119
Tables……………………………………………………………………………131
Figures…………………………………………………………………………...133
References…………………………………………………………………………147

Chapter I
References
1. Glass AG, Lacey JV, Jr., Carreon JD, Hoover RN. Breast cancer incidence, 1980-2006: combined roles of menopausal hormone therapy, screening mammography, and estrogen receptor status. J Natl Cancer Inst 2007;99(15):1152-61.
2. Siegel RL, Miller KD, Jemal A. Cancer statistics, 2016. CA Cancer J Clin 2016;66(1):7-30.
3. Lachapelle J, Foulkes WD. Triple-negative and basal-like breast cancer: implications for oncologists. Curr Oncol 2011;18(4):161-4.
4. Bertucci F, Finetti P, Birnbaum D. Basal breast cancer: a complex and deadly molecular subtype. Curr Mol Med 2012;12(1):96-110.
5. Yeo B, Turner NC, Jones A. An update on the medical management of breast cancer. BMJ 2014;348:g3608 doi 10.1136/bmj.g3608.
6. Gu G, Dustin D, Fuqua SA. Targeted therapy for breast cancer and molecular mechanisms of resistance to treatment. Curr Opin Pharmacol 2016;31:97-103.
7. De Laurentiis M, Cianniello D, Caputo R, Stanzione B, Arpino G, Cinieri S, et al. Treatment of triple negative breast cancer (TNBC): current options and future perspectives. Cancer Treat Rev 2010;36 Suppl 3:S80-6 doi 10.1016/S0305-7372(10)70025-6.
8. Gluz O, Liedtke C, Gottschalk N, Pusztai L, Nitz U, Harbeck N. Triple-negative breast cancer--current status and future directions. Ann Oncol 2009;20(12):1913-27.
9. Pages G, Pouyssegur J. Transcriptional regulation of the Vascular Endothelial Growth Factor gene--a concert of activating factors. Cardiovasc Res 2005;65(3):564-73.
10. Matsumura A, Kubota T, Taiyoh H, Fujiwara H, Okamoto K, Ichikawa D, et al. HGF regulates VEGF expression via the c-Met receptor downstream pathways, PI3K/Akt, MAPK and STAT3, in CT26 murine cells. Int J Oncol 2013;42(2):535-42.
11. Lo HW, Hsu SC, Ali-Seyed M, Gunduz M, Xia W, Wei Y, et al. Nuclear interaction of EGFR and STAT3 in the activation of the iNOS/NO pathway. Cancer Cell 2005;7(6):575-89.
12. Changavi AA, Shashikala A, Ramji AS. Epidermal Growth Factor Receptor Expression in Triple Negative and Nontriple Negative Breast Carcinomas. J Lab Physicians 2015;7(2):79-83.
13. Ho-Yen CM, Jones JL, Kermorgant S. The clinical and functional significance of c-Met in breast cancer: a review. Breast Cancer Res 2015;17:52 doi 10.1186/s13058-015-0547-6.
14. Kim YJ, Choi JS, Seo J, Song JY, Lee SE, Kwon MJ, et al. MET is a potential target for use in combination therapy with EGFR inhibition in triple-negative/basal-like breast cancer. Int J Cancer 2014;134(10):2424-36.
15. Aigner S, Sthoeger ZM, Fogel M, Weber E, Zarn J, Ruppert M, et al. CD24, a mucin-type glycoprotein, is a ligand for P-selectin on human tumor cells. Blood 1997;89(9):3385-95.
16. Friederichs J, Zeller Y, Hafezi-Moghadam A, Grone HJ, Ley K, Altevogt P. The CD24/P-selectin binding pathway initiates lung arrest of human A125 adenocarcinoma cells. Cancer Res 2000;60(23):6714-22.
17. Koedam JA, Cramer EM, Briend E, Furie B, Furie BC, Wagner DD. P-selectin, a granule membrane protein of platelets and endothelial cells, follows the regulated secretory pathway in AtT-20 cells. J Cell Biol 1992;116(3):617-25.
18. Bretz NP, Salnikov AV, Perne C, Keller S, Wang X, Mierke CT, et al. CD24 controls Src/STAT3 activity in human tumors. Cell Mol Life Sci 2012;69(22):3863-79.
19. Baumann P, Thiele W, Cremers N, Muppala S, Krachulec J, Diefenbacher M, et al. CD24 interacts with and promotes the activity of c-src within lipid rafts in breast cancer cells, thereby increasing integrin-dependent adhesion. Cell Mol Life Sci 2012;69(3):435-48.
20. Sammar M, Gulbins E, Hilbert K, Lang F, Altevogt P. Mouse CD24 as a signaling molecule for integrin-mediated cell binding: functional and physical association with src-kinases. Biochem Biophys Res Commun 1997;234(2):330-4.
21. Chan SH, Huang WC, Chang JW, Chang KJ, Kuo WH, Wang MY, et al. MicroRNA-149 targets GIT1 to suppress integrin signaling and breast cancer metastasis. Oncogene 2014;33(36):4496-507.
22. Durandy A, Brousse N, Rozenberg F, De Saint Basile G, Fischer AM, Fischer A. Control of human B cell tumor growth in severe combined immunodeficiency mice by monoclonal anti-B cell antibodies. J Clin Invest 1992;90(3):945-52.
23. Fischer A, Blanche S, Le Bidois J, Bordigoni P, Garnier JL, Niaudet P, et al. Anti-B-cell monoclonal antibodies in the treatment of severe B-cell lymphoproliferative syndrome following bone marrow and organ transplantation. N Engl J Med 1991;324(21):1451-6.
24. Benkerrou M, Jais JP, Leblond V, Durandy A, Sutton L, Bordigoni P, et al. Anti-B-cell monoclonal antibody treatment of severe posttransplant B-lymphoproliferative disorder: prognostic factors and long-term outcome. Blood 1998;92(9):3137-47.
25. Chen YL, Chan SH, Lin PY, Chu PY. The expression of a tumor suppressor gene JDP2 and its prognostic value in hepatocellular carcinoma (HCC) patients. Hum Pathol 2017 doi 10.1016/j.humpath.2017.03.003.
26. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 2005;102(43):15545-50.
27. Ma XJ, Wang Z, Ryan PD, Isakoff SJ, Barmettler A, Fuller A, et al. A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell 2004;5(6):607-16.
28. Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 2012;486(7403):346-52.
29. Han S, Khuri FR, Roman J. Fibronectin stimulates non-small cell lung carcinoma cell growth through activation of Akt/mammalian target of rapamycin/S6 kinase and inactivation of LKB1/AMP-activated protein kinase signal pathways. Cancer research 2006;66(1):315-23.
30. Chan SH, Wang LH. Regulation of cancer metastasis by microRNAs. J Biomed Sci 2015;22:9 doi 10.1186/s12929-015-0113-7.
31. Carmeliet P, Jain RK. Molecular mechanisms and clinical applications of angiogenesis. Nature 2011;473(7347):298-307.
32. Tammela T, Alitalo K. Lymphangiogenesis: Molecular mechanisms and future promise. Cell 2010;140(4):460-76.
33. Hicklin DJ, Ellis LM. Role of the vascular endothelial growth factor pathway in tumor growth and angiogenesis. J Clin Oncol 2005;23(5):1011-27.
34. Loureiro RM, D'Amore PA. Transcriptional regulation of vascular endothelial growth factor in cancer. Cytokine Growth Factor Rev 2005;16(1):77-89 doi 10.1016/j.cytogfr.2005.01.005.
35. Hunziker W, Geuze HJ. Intracellular trafficking of lysosomal membrane proteins. Bioessays 1996;18(5):379-89.
36. Overdevest JB, Thomas S, Kristiansen G, Hansel DE, Smith SC, Theodorescu D. CD24 offers a therapeutic target for control of bladder cancer metastasis based on a requirement for lung colonization. Cancer Res 2011;71(11):3802-11.
37. Fillmore CM, Kuperwasser C. Human breast cancer cell lines contain stem-like cells that self-renew, give rise to phenotypically diverse progeny and survive chemotherapy. Breast Cancer Res 2008;10(2):R25 doi 10.1186/bcr1982.
38. Sheridan C, Kishimoto H, Fuchs RK, Mehrotra S, Bhat-Nakshatri P, Turner CH, et al. CD44+/CD24- breast cancer cells exhibit enhanced invasive properties: an early step necessary for metastasis. Breast Cancer Res 2006;8(5):R59 doi 10.1186/bcr1610.
39. Ricardo S, Vieira AF, Gerhard R, Leitao D, Pinto R, Cameselle-Teijeiro JF, et al. Breast cancer stem cell markers CD44, CD24 and ALDH1: expression distribution within intrinsic molecular subtype. J Clin Pathol 2011;64(11):937-46.
40. Ginestier C, Hur MH, Charafe-Jauffret E, Monville F, Dutcher J, Brown M, et al. ALDH1 is a marker of normal and malignant human mammary stem cells and a predictor of poor clinical outcome. Cell Stem Cell 2007;1(5):555-67.
41. Baumann P, Cremers N, Kroese F, Orend G, Chiquet-Ehrismann R, Uede T, et al. CD24 expression causes the acquisition of multiple cellular properties associated with tumor growth and metastasis. Cancer Res 2005;65(23):10783-93.
42. Bircan S, Kapucuoglu N, Baspinar S, Inan G, Candir O. CD24 expression in ductal carcinoma in situ and invasive ductal carcinoma of breast: an immunohistochemistry-based pilot study. Pathol Res Pract 2006;202(8):569-76.
43. Shipitsin M, Campbell LL, Argani P, Weremowicz S, Bloushtain-Qimron N, Yao J, et al. Molecular definition of breast tumor heterogeneity. Cancer Cell 2007;11(3):259-73.
44. Niu G, Wright KL, Huang M, Song L, Haura E, Turkson J, et al. Constitutive Stat3 activity up-regulates VEGF expression and tumor angiogenesis. Oncogene 2002;21(13):2000-8.
45. Song L, Turkson J, Karras JG, Jove R, Haura EB. Activation of Stat3 by receptor tyrosine kinases and cytokines regulates survival in human non-small cell carcinoma cells. Oncogene 2003;22(27):4150-65.
46. Tyan SW, Kuo WH, Huang CK, Pan CC, Shew JY, Chang KJ, et al. Breast cancer cells induce cancer-associated fibroblasts to secrete hepatocyte growth factor to enhance breast tumorigenesis. PLoS One 2011;6(1):e15313 doi 10.1371/journal.pone.0015313.
47. Goswami S, Sahai E, Wyckoff JB, Cammer M, Cox D, Pixley FJ, et al. Macrophages promote the invasion of breast carcinoma cells via a colony-stimulating factor-1/epidermal growth factor paracrine loop. Cancer Res 2005;65(12):5278-83.
48. Deng X, Apple S, Zhao H, Song J, Lee M, Luo W, et al. CD24 Expression and differential resistance to chemotherapy in triple-negative breast cancer. Oncotarget 2017;8(24):38294-308.


Chapter II
References
1. Chan SH, Tsai KW, Chiu SY, Kuo WH, Chen HY, Jiang SS, et al. Identification of the Novel Role of CD24 as an Oncogenesis Regulator and Therapeutic Target for Triple-Negative Breast Cancer. Mol Cancer Ther. 2019;18(1):147-61.
2. Nakayasu ES, Yashunsky DV, Nohara LL, Torrecilhas AC, Nikolaev AV, Almeida IC. GPIomics: global analysis of glycosylphosphatidylinositol-anchored molecules of Trypanosoma cruzi. Mol Syst Biol. 2009;5:261.


Chapter III
References:
1. Bray F, Ferlay J, Soerjomataram I, Siegel RL, Torre LA, Jemal A: Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin 2018, 68(6):394-424.
2. Yeo B, Turner NC, Jones A: An update on the medical management of breast cancer. BMJ 2014, 348:g3608.
3. Bertucci F, Finetti P, Birnbaum D: Basal breast cancer: a complex and deadly molecular subtype. Curr Mol Med 2012, 12(1):96-110.
4. Derrien T, Guigo R, Johnson R: The Long Non-Coding RNAs: A New (P)layer in the "Dark Matter". Front Genet 2011, 2:107.
5. Fenoglio C, Ridolfi E, Galimberti D, Scarpini E: An emerging role for long non-coding RNA dysregulation in neurological disorders. Int J Mol Sci 2013, 14(10):20427-20442.
6. Kumar MM, Goyal R: LncRNA as a Therapeutic Target for Angiogenesis. Curr Top Med Chem 2017, 17(15):1750-1757.
7. Serviss JT, Johnsson P, Grander D: An emerging role for long non-coding RNAs in cancer metastasis. Front Genet 2014, 5:234.
8. Yoon JH, Abdelmohsen K, Gorospe M: Functional interactions among microRNAs and long noncoding RNAs. Semin Cell Dev Biol 2014, 34:9-14.
9. Chan JJ, Tay Y: Noncoding RNA:RNA Regulatory Networks in Cancer. Int J Mol Sci 2018, 19(5).
10. Moses H, Barcellos-Hoff MH: TGF-beta biology in mammary development and breast cancer. Cold Spring Harb Perspect Biol 2011, 3(1):a003277.
11. Howe LR, Brown AM: Wnt signaling and breast cancer. Cancer Biol Ther 2004, 3(1):36-41.
12. Xu J, Lamouille S, Derynck R: TGF-beta-induced epithelial to mesenchymal transition. Cell Res 2009, 19(2):156-172.
13. Pohl SG, Brook N, Agostino M, Arfuso F, Kumar AP, Dharmarajan A: Wnt signaling in triple-negative breast cancer. Oncogenesis 2017, 6(4):e310.
14. Lindvall C, Bu W, Williams BO, Li Y: Wnt signaling, stem cells, and the cellular origin of breast cancer. Stem Cell Rev 2007, 3(2):157-168.
15. Chan SH, Huang WC, Chang JW, Chang KJ, Kuo WH, Wang MY, Lin KY, Uen YH, Hou MF, Lin CM et al: MicroRNA-149 targets GIT1 to suppress integrin signaling and breast cancer metastasis. Oncogene 2014, 33(36):4496-4507.
16. Jeong JS, Jiang L, Albino E, Marrero J, Rho HS, Hu J, Hu S, Vera C, Bayron-Poueymiroy D, Rivera-Pacheco ZA et al: Rapid identification of monospecific monoclonal antibodies using a human proteome microarray. Molecular & cellular proteomics : MCP 2012, 11(6):O111 016253.
17. Fan B, Lu KY, Reymond Sutandy FX, Chen YW, Konan K, Zhu H, Kao CC, Chen CS: A human proteome microarray identifies that the heterogeneous nuclear ribonucleoprotein K (hnRNP K) recognizes the 5' terminal sequence of the hepatitis C virus RNA. Molecular & cellular proteomics : MCP 2014, 13(1):84-92.
18. Fang LL, Sun BF, Huang LR, Yuan HB, Zhang S, Chen J, Yu ZJ, Luo H: Potent Inhibition of miR-34b on Migration and Invasion in Metastatic Prostate Cancer Cells by Regulating the TGF-beta Pathway. Int J Mol Sci 2017, 18(12).
19. Siemens H, Jackstadt R, Hunten S, Kaller M, Menssen A, Gotz U, Hermeking H: miR-34 and SNAIL form a double-negative feedback loop to regulate epithelial-mesenchymal transitions. Cell Cycle 2011, 10(24):4256-4271.
20. Bray F, Ren JS, Masuyer E, Ferlay J: Global estimates of cancer prevalence for 27 sites in the adult population in 2008. International journal of cancer 2013, 132(5):1133-1145.
21. Siegel RL, Miller KD, Jemal A: Cancer statistics, 2016. CA: a cancer journal for clinicians 2016, 66(1):7-30.
22. Schmitt AM, Chang HY: Long noncoding RNAs in cancer pathways. Cancer Cell 2016, 29(4):452-463.
23. Wapinski O, Chang HY: Long noncoding RNAs and human disease. Trends in cell biology 2011, 21(6):354-361.
24. Mourtada-Maarabouni M, Pickard M, Hedge V, Farzaneh F, Williams G: GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer. Oncogene 2009, 28(2):195-208.
25. Adriaenssens E, Dumont L, Lottin S, Bolle D, Leprêtre A, Delobelle A, Bouali F, Dugimont T, Coll J, Curgy J-J: H19 overexpression in breast adenocarcinoma stromal cells is associated with tumor values and steroid receptor status but independent of p53 and Ki-67 expression. The American journal of pathology 1998, 153(5):1597-1607.
26. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E: Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007, 129(7):1311-1323.
27. Loi S, Haibe-Kains B, Desmedt C, Lallemand F, Tutt AM, Gillet C, Ellis P, Harris A, Bergh J, Foekens JA: Definition of clinically distinct molecular subtypes in estrogen receptor–positive breast carcinomas through genomic grade. Journal of clinical oncology 2007, 25(10):1239-1246.
28. Silva JM, Boczek NJ, Berres MW, Ma X, Smith DI: LSINCT5 is over expressed in breast and ovarian cancer and affects cellular proliferation. RNA biology 2011, 8(3):496-505.
29. Wang F, Li X, Xie X, Zhao L, Chen W: UCA1, a non‐protein‐coding RNA up‐regulated in bladder carcinoma and embryo, influencing cell growth and promoting invasion. FEBS letters 2008, 582(13):1919-1927.
30. Benoît M-H, Hudson TJ, Maire G, Squire JA, Arcand SL, Provencher D, Mes-Masson A-M, Tonin PN: Global analysis of chromosome X gene expression in primary cultures of normal ovarian surface epithelial cells and epithelial ovarian cancer cell lines. International journal of oncology 2007, 30(1):5-18.
31. Godinho M, Meijer D, Setyono‐Han B, Dorssers LC, van Agthoven T: Characterization of BCAR4, a novel oncogene causing endocrine resistance in human breast cancer cells. Journal of cellular physiology 2011, 226(7):1741-1749.
32. Yang L, Tang Y, He Y, Wang Y, Lian Y, Xiong F, Shi L, Zhang S, Gong Z, Zhou Y: High Expression of LINC01420 indicates an unfavorable prognosis and modulates cell migration and invasion in nasopharyngeal carcinoma. Journal of Cancer 2017, 8(1):97.
33. Dey BK, Mueller AC, Dutta A: Long non-coding RNAs as emerging regulators of differentiation, development, and disease. Transcription 2014, 5(4):e944014.
34. Kawakami T, Zhang C, Taniguchi T, Kim CJ, Okada Y, Sugihara H, Hattori T, Reeve AE, Ogawa O, Okamoto K: Characterization of loss-of-inactive X in Klinefelter syndrome and female-derived cancer cells. Oncogene 2004, 23(36):6163-6169.
35. Ren C, Li X, Wang T, Wang G, Zhao C, Liang T, Zhu Y, Li M, Yang C, Zhao Y: Functions and mechanisms of long noncoding RNAs in ovarian cancer. International journal of gynecological cancer 2015, 25(4):566-569.
36. Tantai J, Hu D, Yang Y, Geng J: Combined identification of long non-coding RNA XIST and HIF1A-AS1 in serum as an effective screening for non-small cell lung cancer. International journal of clinical and experimental pathology 2015, 8(7):7887.
37. Yao Y, Ma J, Xue Y, Wang P, Li Z, Liu J, Chen L, Xi Z, Teng H, Wang Z: Knockdown of long non-coding RNA XIST exerts tumor-suppressive functions in human glioblastoma stem cells by up-regulating miR-152. Cancer letters 2015, 359(1):75-86.
38. Zhu Z, Liang Z, Liany H, Yang C, Wen L, Lin Z, Sheng Y, Lin Y, Ye L, Cheng Y: Discovery of a novel genetic susceptibility locus on X chromosome for systemic lupus erythematosus. Arthritis research & therapy 2015, 17(1):349.
39. Brooks WH, Renaudineau Y: Epigenetics and autoimmune diseases: the X chromosome-nucleolus nexus. Frontiers in genetics 2015, 6:22.
40. Toren P, Zoubeidi A: Targeting the PI3K/Akt pathway in prostate cancer: Challenges and opportunities (Review). International journal of oncology 2014, 45(5):1793-1801.
41. Wilusz JE, Sunwoo H, Spector DL: Long noncoding RNAs: functional surprises from the RNA world. Genes & development 2009, 23(13):1494-1504.
42. Barnum KJ, O’Connell MJ: Cell cycle regulation by checkpoints. Cell Cycle Control: Mechanisms and Protocols 2014:29-40.
43. De Boer L, Oakes V, Beamish H, Giles N, Stevens F, Somodevilla-Torres M, DeSouza C, Gabrielli B: Cyclin A/cdk2 coordinates centrosomal and nuclear mitotic events. Oncogene 2008, 27(31):4261-4268.
44. Gavet O, Pines J: Progressive activation of CyclinB1-Cdk1 coordinates entry to mitosis. Developmental cell 2010, 18(4):533-543.
45. Santamaría D, Barrière C, Cerqueira A, Hunt S, Tardy C, Newton K, Cáceres JF, Dubus P, Malumbres M, Barbacid M: Cdk1 is sufficient to drive the mammalian cell cycle. Nature 2007, 448(7155):811-815.
46. Elledge SJ: Cell cycle checkpoints: preventing an identity crisis. Science (New York, NY 1996, 274(5293):1664.
47. Sørensen CS, Syljuåsen RG: Safeguarding genome integrity: the checkpoint kinases ATR, CHK1 and WEE1 restrain CDK activity during normal DNA replication. Nucleic acids research 2012, 40(2):477-486.
48. Watanabe N, Broome M, Hunter T: Regulation of the human WEE1Hu CDK tyrosine 15-kinase during the cell cycle. The EMBO journal 1995, 14(9):1878.
49. Tyagi A, Singh RP, Agarwal C, Siriwardana S, Sclafani RA, Agarwal R: Resveratrol causes Cdc2-tyr15 phosphorylation via ATM/ATR–Chk1/2–Cdc25C pathway as a central mechanism for S phase arrest in human ovarian carcinoma Ovcar-3 cells. Carcinogenesis 2005, 26(11):1978-1987.