Open Access

Retrospective screening of microarray data to identify candidate IFN-inducible genes in a HTLV-1 transformed model

  • Authors:
    • Alaa Refaat
    • Mohamed Owis
    • Sherif Abdelhamed
    • Ikuo Saiki
    • Hiroaki Sakurai
  • View Affiliations

  • Published online on: February 9, 2018     https://doi.org/10.3892/ol.2018.8014
  • Pages: 4753-4758
  • Copyright: © Refaat et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

Metrics: HTML 0 views | PDF 0 views     Cited By (CrossRef): 0 citations

Abstract

HuT-102 cells are considered one of the most representable human T-lymphotropic virus 1 (HTLV-1)-infected cell lines for studying adult T‑cell lymphoma (ATL). In our previous studies, genome‑wide screening was performed using the GeneChip system with Human Genome Array U133 Plus 2.0 for transforming growth factor‑β‑activated kinase 1 (TAK1)‑, interferon regulatory factor 3 (IRF3)‑ and IRF4‑regulated genes to demonstrate the effects of interferon‑inducible genes in HuT‑102 cells. Our previous findings demonstrated that TAK1 induced interferon inducible genes via an IRF3‑dependent pathway and that IRF4 has a counteracting effect. As our previous data was performed by manual selection of common interferon‑related genes mentioned in the literature, there has been some obscure genes that have not been considered. In an attempt to maximize the outcome of those microarrays, the present study reanalyzed the data collected in previous studies through a set of computational rules implemented using ‘R’ software, to identify important candidate genes that have been missed in the previous two studies. The final list obtained consisted of ten genes that are highly recommend as potential candidate for therapies targeting the HTLV‑1 infected cancer cells. Those genes are ATM, CFTR, MUC4, PARP14, QK1, UBR2, CLEC7A (Dectin‑1), L3MBTL, SEC24D and TMEM140. Notably, PARP14 has gained increased attention as a promising target in cancer cells.

References

1 

Coffin JM: The discovery of HTLV-1, the first pathogenic human retrovirus. Proc Natl Acad Sci USA. 112:15525–15529. 2015. View Article : Google Scholar : PubMed/NCBI

2 

Poiesz BJ, Ruscetti FW, Gazdar AF, Bunn PA, Minna JD and Gallo RC: Detection and isolation of type C retrovirus particles from fresh and cultured lymphocytes of a patient with cutaneous T-cell lymphoma. Proc Natl Acad Sci USA. 77:7415–7419. 1980. View Article : Google Scholar : PubMed/NCBI

3 

Refaat A, Zhou Y, Suzuki S, Takasaki I, Koizumi K, Yamaoka S, Tabuchi Y, Saiki I and Sakurai H: Distinct roles of transforming growth factor-beta-activated kinase 1 (TAK1)-c-Rel and interferon regulatory factor 4 (IRF4) pathways in human T cell lymphotropic virus 1-transformed T helper 17 cells producing interleukin-9. J Biol Chem. 286:21092–21099. 2011. View Article : Google Scholar : PubMed/NCBI

4 

Suzuki S, Zhou Y, Refaat A, Takasaki I, Koizumi K, Yamaoka S, Tabuchi Y, Saiki I and Sakurai H: Human T cell lymphotropic virus 1 manipulates interferon regulatory signals by controlling the TAK1-IRF3 and IRF4 pathways. J Biol Chem. 285:4441–4446. 2010. View Article : Google Scholar : PubMed/NCBI

5 

Lee JH and Paull TT: Activation and regulation of ATM kinase activity in response to DNA double-strand breaks. Oncogene. 26:7741–7748. 2007. View Article : Google Scholar : PubMed/NCBI

6 

Huang X, Halicka HD and Darzynkiewicz Z: Detection of histone H2AX phosphorylation on Ser-139 as an indicator of DNA damage (DNA double-strand breaks). Curr Protoc Cytom Chapter. 7:Unit 7.27. 2004. View Article : Google Scholar

7 

Canman CE, Lim DS, Cimprich KA, Taya Y, Tamai K, Sakaguchi K, Appella E, Kastan MB and Siliciano JD: Activation of the ATM kinase by ionizing radiation and phosphorylation of p53. Science. 281:1677–1679. 1998. View Article : Google Scholar : PubMed/NCBI

8 

Ahmed M and Rahman N: ATM and breast cancer susceptibility. Oncogene. 25:5906–5911. 2006. View Article : Google Scholar : PubMed/NCBI

9 

Gadsby DC, Vergani P and Csanády L: The ABC protein turned chloride channel whose failure causes cystic fibrosis. Nature. 440:477–483. 2006. View Article : Google Scholar : PubMed/NCBI

10 

Jones AM and Helm JM: Emerging treatments in cystic fibrosis. Drugs. 69:1903–1910. 2009. View Article : Google Scholar : PubMed/NCBI

11 

Than BLN, Linnekamp JF, Starr TK, Largaespada DA, Rod A, Zhang Y, Bruner V, Abrahante J, Schumann A, Luczak T, et al: CFTR is a tumor suppressor gene in murine and human intestinal cancer. Oncogene. 36:35042017. View Article : Google Scholar : PubMed/NCBI

12 

Xie C, Jiang XH, Zhang JT, Sun TT, Dong JD, Sanders AJ, Diao RY, Wang Y, Fok KL, Tsang LL, et al: CFTR suppresses tumor progression through miR-193b targeting urokinase plasminogen activator (uPA) in prostate cancer. Oncogene. 32:2282–2291, 2291.e1-7. 2013. View Article : Google Scholar : PubMed/NCBI

13 

Xu J, Yong M, Li J, Dong X, Yu T, Fu X and Hu L: High level of CFTR expression is associated with tumor aggression and knockdown of CFTR suppresses proliferation of ovarian cancer in vitro and in vivo. Oncol Rep. 33:2227–2234. 2015. View Article : Google Scholar : PubMed/NCBI

14 

Zhang JT, Jiang XH, Xie C, Cheng H, Da Dong J, Wang Y, Fok KL, Zhang XH, Sun TT, Tsang LL, et al: Downregulation of CFTR promotes epithelial-to-mesenchymal transition and is associated with poor prognosis of breast cancer. Biochim Biophys Acta. 1833:2961–2969. 2013. View Article : Google Scholar : PubMed/NCBI

15 

Jhala N, Jhala D, Vickers SM, Eltoum I, Batra SK, Manne U, Eloubeidi M, Jones JJ and Grizzle WE: Biomarkers in Diagnosis of pancreatic carcinoma in fine-needle aspirates. Am J Clin Pathol. 126:572–579. 2006. View Article : Google Scholar : PubMed/NCBI

16 

Srivastava SK, Bhardwaj A, Singh S, Arora S, Wang B, Grizzle WE and Singh AP: MicroRNA-150 directly targets MUC4 and suppresses growth and malignant behavior of pancreatic cancer cells. Carcinogenesis. 32:1832–1839. 2011. View Article : Google Scholar : PubMed/NCBI

17 

Mehrotra P, Riley JP, Patel R, Li F, Voss L and Goenka S: PARP-14 functions as a transcriptional switch for Stat6-dependent gene activation. J Biol Chem. 286:1767–1776. 2011. View Article : Google Scholar : PubMed/NCBI

18 

Iansante V, Choy PM, Fung SW, Liu Y, Chai JG, Dyson J, Del Rio A, D'Santos C, Williams R, Chokshi S, et al: PARP14 promotes the Warburg effect in hepatocellular carcinoma by inhibiting JNK1-dependent PKM2 phosphorylation and activation. Nat Commun. 6:78822015. View Article : Google Scholar : PubMed/NCBI

19 

Aberg K, Saetre P, Jareborg N and Jazin E: Human QKI, a potential regulator of mRNA expression of human oligodendrocyte-related genes involved in schizophrenia. Proc Natl Acad Sci USA. 103:7482–7487. 2006. View Article : Google Scholar : PubMed/NCBI

20 

Zong FY, Fu X, Wei WJ, Luo YG, Heiner M, Cao LJ, Fang Z, Fang R, Lu D, Ji H and Hui J: The RNA-binding protein QKI suppresses cancer-associated aberrant splicing. PLoS Genet. 10:e10042892014. View Article : Google Scholar : PubMed/NCBI

21 

Chen AJ, Paik JH, Zhang H, Shukla SA, Mortensen R, Hu J, Ying H, Hu B, Hurt J, Farny N, et al: STAR RNA-binding protein Quaking suppresses cancer via stabilization of specific miRNA. Genes Dev. 26:1459–1472. 2012. View Article : Google Scholar : PubMed/NCBI

22 

Kume K, Iizumi Y, Shimada M, Ito Y, Kishi T, Yamaguchi Y and Handa H: Role of N-end rule ubiquitin ligases UBR1 and UBR2 in regulating the leucine-mTOR signaling pathway. Genes Cells. 15:339–349. 2010. View Article : Google Scholar : PubMed/NCBI

23 

Taylor PR, Brown GD, Reid DM, Willment JA, Martinez-Pomares L, Gordon S and Wong SY: The beta-glucan receptor, dectin-1, is predominantly expressed on the surface of cells of the monocyte/macrophage and neutrophil lineages. J Immunol. 169:3876–3882. 2002. View Article : Google Scholar : PubMed/NCBI

24 

Huysamen C and Brown GD: The fungal pattern recognition receptor, Dectin-1, and the associated cluster of C-type lectin-like receptors. FEMS Microbiol Lett. 290:121–128. 2009. View Article : Google Scholar : PubMed/NCBI

25 

Saijo S and Iwakura Y: Dectin-1 and Dectin-2 in innate immunity against fungi. Int Immunol. 23:467–472. 2011. View Article : Google Scholar : PubMed/NCBI

26 

Activation of Dectin-1 on Macrophages Promotes Pancreatic Cancer. Cancer Discov. 7:5492017.

27 

Li J, Bench AJ, Vassiliou GS, Fourouclas N, Ferguson-Smith AC and Green AR: Imprinting of the human L3MBTL gene, a polycomb family member located in a region of chromosome 20 deleted in human myeloid malignancies. Proc Natl Acad Sci USA. 101:7341–7346. 2004. View Article : Google Scholar : PubMed/NCBI

28 

Pagano A, Letourneur F, Garcia-Estefania D, Carpentier JL, Orci L and Paccaud JP: Sec24 proteins and sorting at the endoplasmic reticulum. J Biol Chem. 274:7833–7840. 1999. View Article : Google Scholar : PubMed/NCBI

29 

Li B, Huang MZ, Wang XQ, Tao BB, Zhong J, Wang XH, Zhang WC and Li ST: TMEM140 is associated with the prognosis of glioma by promoting cell viability and invasion. J Hematol Oncol. 8:892015. View Article : Google Scholar : PubMed/NCBI

30 

Camicia R, Winkler HC and Hassa PO: Novel drug targets for personalized precision medicine in relapsed/refractory diffuse large B-cell lymphoma: A comprehensive review. Mol Cancer. 14:2072015. View Article : Google Scholar : PubMed/NCBI

Related Articles

Journal Cover

April 2018
Volume 15 Issue 4

Print ISSN: 1792-1074
Online ISSN:1792-1082

Sign up for eToc alerts

Recommend to Library

Copy and paste a formatted citation
APA
Refaat, A., Owis, M., Abdelhamed, S., Saiki, I., & Sakurai, H. (2018). Retrospective screening of microarray data to identify candidate IFN-inducible genes in a HTLV-1 transformed model. Oncology Letters, 15, 4753-4758. https://doi.org/10.3892/ol.2018.8014
MLA
Refaat, A., Owis, M., Abdelhamed, S., Saiki, I., Sakurai, H."Retrospective screening of microarray data to identify candidate IFN-inducible genes in a HTLV-1 transformed model". Oncology Letters 15.4 (2018): 4753-4758.
Chicago
Refaat, A., Owis, M., Abdelhamed, S., Saiki, I., Sakurai, H."Retrospective screening of microarray data to identify candidate IFN-inducible genes in a HTLV-1 transformed model". Oncology Letters 15, no. 4 (2018): 4753-4758. https://doi.org/10.3892/ol.2018.8014