Chromosomal Location of Genes Differentially Expressed in Tumor Cells Surviving High-Dose X-ray Irradiation: A Preliminary Study on Radio-Fragile Sites
Abstract
:1. Introduction
2. Materials and Methods
2.1. Cell Culture
2.2. Subcloning for MCF7-IR Cells
2.3. Colony Formation Assay
2.4. DNA Microarray Analysis
2.5. Data Analysis
2.6. Irradiated Condition
2.7. Statistical Analysis
3. Results
3.1. Radio-Sensitivity of IR Cells
3.2. Chromosomal Location of Upregulated Genes in IR Cells from Microarray Data
3.3. Functional Categories of Altered Genes
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Hall, E.J.; Brenner, D.J. Cancer Risks from Diagnostic Radiology. Br. J. Radiol. 2008, 81, 362–378. [Google Scholar] [CrossRef] [PubMed]
- Martin, C.J.; Sutton, D.G.; West, C.M.; Wright, E.G. The Radiobiology/Radiation Protection Interface in Healthcare. J. Radiol. Prot. 2009, 29, A1. [Google Scholar] [CrossRef] [Green Version]
- Matsuya, Y.; Mcmahon, S.J.; Tsutsumi, K.; Sasaki, K.; Yoshii, Y.; Mori, R.; Oikawa, J.; Prise, K.M.; Date, H. Investigation of Dose-Rate Effects and Cell-Cycle Distribution under Protracted Exposure to Ionizing Radiation for Various Dose-Rates. Sci. Rep. 2018, 8, 8287. [Google Scholar] [CrossRef] [Green Version]
- Killcoyne, S.; Yusuf, A.; Fitzgerald, R.C. Genomic Instability Signals Offer Diagnostic Possibility in Early Cancer Detection. Trends Genet. 2021. [Google Scholar] [CrossRef] [PubMed]
- Kuwabara, M.; Takahashi, K.; Inanami, O. Induction of Apoptosis through the Activation of SAPK/JNK Followed by the Expression of Death Receptor Fas in X-Irradiated Cells. J. Radiat. Res. 2003, 44, 203–209. [Google Scholar] [CrossRef]
- Van Gent, D.C.; Hoeijmakers, J.H.J.; Kanaar, R. Chromosomal Stability and the DNA Double-Stranded Break Connection. Nat. Rev. Genet. 2001, 2, 196–206. [Google Scholar] [CrossRef]
- Tsutsumi, K.; Yasuda, M.; Nishioka, T. X-ray Irradiation Altered Chemosensitivity of a P53-Null Non-Small Cell Lung Cancer Cell Line. Cell Struct. Funct. 2006, 31, 47–52. [Google Scholar] [CrossRef] [Green Version]
- Tsutsumi, K.; Tsuda, M.; Yazawa, N.; Nakamura, H.; Ishihara, S.; Haga, H.; Yasuda, M.; Yamazaki, R.; Shirato, H.; Kawaguchi, H.; et al. Increased Motility and Invasiveness in Tumor Cells That Survive 10 Gy Irradiation. Cell Struct. Funct. 2009, 34, 89–96. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Muradyan, A.; Gilbertz, K.; Stabentheiner, S.; Klause, S.; Madle, H.; Meineke, V.; Ullmann, R.; Scherthan, H. Acute High-Dose X-Radiation-Induced Genomic Changes in A549 Cells. Radiat. Res. 2011, 175, 700–707. [Google Scholar] [CrossRef] [PubMed]
- Sarni, D.; Sasaki, T.; Irony Tur-Sinai, M.; Miron, K.; Rivera-Mulia, J.C.; Magnuson, B.; Ljungman, M.; Gilbert, D.M.; Kerem, B. 3D Genome Organization Contributes to Genome Instability at Fragile Sites. Nat. Commun. 2020, 11, 3613. [Google Scholar] [CrossRef] [PubMed]
- Wu, H. Probabilities of Radiation-Induced Inter- and Intrachromosomal Exchanges and Their Dependence on the DNA Content of the Chromosome. Radiat. Res. 2001, 156, 603–606. [Google Scholar] [CrossRef]
- Matsuya, Y.; Ohtsubo, Y.; Tsutsumi, K.; Sasaki, K.; Yamazaki, R.; Date, H. Quantitative Estimation of DNA Damage by Photon Irradiation Based on the Microdosimetric-Kinetic Model. J. Radiat. Res. 2014, 55, 484–493. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Fechter, A.; Buettel, I.; Kuehnel, E.; Schwab, M.; Savelyeva, L. Cloning of Genetically Tagged Chromosome Break Sequences Reveals New Fragile Sites at 6p21 and 13q22. Int. J. Cancer 2007, 120, 2359–2367. [Google Scholar] [CrossRef]
- Demirhan, O.; Taştemir, D. Cytogenetic Effects of Ethanol on Chronic Alcohol Users. Alcohol. Alcohol. 2008, 43, 127–136. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Gümüş, G.; Sungurolu, A.; Tükün, A.; Sayin, D.B.; Bökesoy, I. Common Fragile Sites Associated with the Breakpoints of Chromosomal Aberrations in Hematologic Neoplasms. Cancer Genet. Cytogenet. 2002, 133, 168–171. [Google Scholar] [CrossRef]
- Zhang, Y.; Matthiesen, P.; Harder, S.; Siebert, R.; Castoldi, G.; Calasanz, M.J.; Wong, K.F.; Rosenwald, A.; Ott, G.; Atkin, N.B.; et al. A 3-CM Commonly Deleted Region in 6q21 in Leukemias and Lymphomas Delineated by Fluorescence In Situ Hybridization. Genes Chromosomes Cancer 2000, 27, 52–58. [Google Scholar] [CrossRef]
- Utada, Y.; Haga, S.; Kajiwara, T.; Kasumi, F.; Sakamoto, G.; Nakamura, Y.; Emi, M. Mapping of Target Regions of Allelic Loss in Primary Breast Cancers to 1-CM Intervals on Genomic Contigs at 6q21 and 6q25.3. Jpn. J. Cancer. Res. 2005, 91, 293–300. [Google Scholar] [CrossRef]
- Anglesio, M.S.; Evdokimova, V.; Melnyk, N.; Zhang, L.; Fernandez, C.V.; Grundy, P.E.; Leach, S.; Marra, M.A.; Brooks-Wilson, A.R.; Penninger, J.; et al. Differential Expression of a Novel Ankyrin Containing E3 Ubiquitin-Protein Ligase, Hace1, in Sporadic Wilms’ Tumor versus Normal Kidney. Hum. Mol. Genet. 2004, 13, 2061–2074. [Google Scholar] [CrossRef] [Green Version]
- Bruce, C.K.; Howard, P.; Nowak, N.J.; Hoban, P.R. Molecular Analysis of Region t(5;6)(Q21;Q21) in Wilms Tumor. Cancer Genet. Cytogenet. 2003, 141, 106–113. [Google Scholar] [CrossRef]
- Forus, A.; Berner, J.M.; Meza-Zepeda, L.A.; Saeter, G.; Mischke, D.; Fodstad, Ø.; Myklebost, O. Molecular Characterization of a Novel Amplicon at 1q21-Q22 Frequently Observed in Human Sarcomas. Br. J. Cancer 1998, 78, 495–503. [Google Scholar] [CrossRef] [Green Version]
- Kudoh, K.; Takano, M.; Koshikawa, T.; Hirai, M.; Yoshida, S.; Mano, Y.; Yamamoto, K.; Ishii, K.; Kita, T.; Kikuchi, Y.; et al. Gains of 1q21-Q22 and 13q12-Q14 Are Potential Indicators for Resistance to Cisplatin-Based Chemotherapy in Ovarian Cancer Patients. Clin. Cancer Res. 1999, 5, 2526–2531. [Google Scholar]
- Hirai, M.; Yoshida, S.; Kashiwagi, H.; Kawamura, T.; Ishikawa, T.; Kaneko, M.; Ohkawa, H.; Nakagawara, A.; Miwa, M.; Uchida, K. 1Q23 Gain Is Associated With Progressive Neuroblastoma Resistant To Aggressive Treatment. Genes Chromosomes Cancer 1999, 25, 261–269. [Google Scholar] [CrossRef]
- Richards, R.I. Fragile and Unstable Chromosomes in Cancer: Causes and Consequences. Trends Genet. 2001, 17, 339–345. [Google Scholar] [CrossRef]
- O’Keefe, L.V.; Richards, R.I. Common Chromosomal Fragile Sites and Cancer: Focus on FRA16D. Cancer Lett. 2006, 232, 37–47. [Google Scholar] [CrossRef]
- Durkin, S.G.; Glover, T.W. Chromosome Fragile Sites. Annu. Rev. Genet. 2007, 41, 169–192. [Google Scholar] [CrossRef] [PubMed]
- Morelli, C.; Karayianni, E.; Magnanini, C.; Mungall, A.J.; Thorland, E.; Negrini, M.; Smith, D.I.; Barbanti-Brodano, G. Cloning and Characterization of the Common Fragile Site FRA6F Harboring a Replicative Senescence Gene and Frequently Deleted in Human Tumors. Oncogene 2002, 21, 7266–7276. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Fritz, A.J.; Sehgal, N.; Pliss, A.; Xu, J.; Berezney, R. Chromosome Territories and the Global Regulation of the Genome. Genes Chromosomes Cancer 2019, 58, 407–426. [Google Scholar] [CrossRef] [Green Version]
- Mahy, N.L.; Perry, P.E.; Gilchrist, S.; Baldock, R.A.; Bickmore, W.A. Spatial Organization of Active and Inactive Genes and Noncoding DNA within Chromosome Territories. J. Cell Biol. 2002, 157, 579–589. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Olivares-Chauvet, P.; Fennessy, D.; Jackson, D.A.; Mendoza, M. Innate Structure of DNA Foci Restricts the Mixing of DNA from Different Chromosome Territories. PLoS ONE 2011, 6, e27527. [Google Scholar] [CrossRef] [Green Version]
H1299 | MCF7 | |||
---|---|---|---|---|
Viability (%) | SEM † | Viability (%) | SEM † | |
Parent | 3.1 × 100 | 0.050 | 2.5 × 10−2 | 0.006 |
IR | 9.8 × 10−1 | 0.135 | 7.5 × 10−3 | 0.003 |
Cell Line | Genes and GenBank Accession No. | Functional Category |
---|---|---|
H1299 | histone 2, H2ab (HIST2H2AB) [NM_175065] | Member of the histone H2A family |
S100 calcium binding protein A16 (S100A16) [NM_080388] | * | |
hypothetical protein LOC200030 (LOC200030) [NM_183372] | * | |
hypothetical protein DJ328E19.C1.1 (DJ328E19.C1.1) [NM_015383] | * | |
phosphoprotein enriched in astrocytes 15 (PEA15) [NM_003768] | Insulin resistance in glucose uptake | |
histone 2, H2aa (HIST2H2AA) [NM_003516] | Member of the histone H2A family | |
hypothetical protein LOC200030 (LOC200030) [NM_183372] | * | |
histone 2, H2be (HIST2H2BE) [NM_003528] | Member of the histone H2B family | |
histone 2, H2ac (HIST2H2AC) [NM_003517] | Member of the histone H2B family | |
small protein effector 1 of Cdc42 (SPEC1) [NM_020239] | * | |
hypothetical protein FLJ20519 (FLJ20519) [NM_017860] | * | |
MCF7 | Notch homolog 2 (Drosophila) N-terminal like (NOTCH2NL), [NM_203458] | * |
cDNA FLJ11946 fis, clone HEMBB1000709 [AK022008] | * | |
late cornified envelope 2C (LCE2C) [NM_178429] | * | |
S100 calcium binding protein A8 (S100A8) [NM_002964] | Cell cycle, progression and differentiation | |
BI026064 CM0-MT0374-060201-774-h11 MT0374 [BI026064] | * | |
small proline-rich protein 3 (SPRR3), transcript variant 1 [NM_005416] | * | |
small proline-rich protein 1A (SPRR1A) [NM_005987] | * | |
S100 calcium binding protein A9 (S100A9) [NM_002965] | Inhibition of casein kinase | |
cathepsin S (CTSS) [NM_004079] | Degradation of the antigenic proteins to peptides on MHC class II | |
S100 calcium binding protein A3 (S100A3) [NM_002960] | * | |
S100 calcium binding protein A2 (S100A2) [NM_005978] | Tumor suppressor function | |
aquaporin 10 (AQP10) [NM_080429] | Water-selective channel |
Cell Line | Genes and GenBank Accession No. | Functionally Category |
---|---|---|
H1299 | histone 1, H1c (HIST1H1C) [NM_005319] | Member of the histoneH1 family |
histone 1, H1d (HIST1H1D) [NM_005320] | Member of the histoneH1 family | |
histone 1, H2bg (HIST1H2BG) [NM_003518] | Member of the histoneH2B family | |
histone 1, H2bf (HIST1H2BF) [NM_003522] | Member of the histoneH2B family | |
histone 1, H2bc (HIST1H2BC) [NM_003526] | Member of the histoneH2B family | |
histone 1, H2be (HIST1H2BE) [NM_003523] | Member of the histoneH2B family | |
histone 1, H2ad (HIST1H2AD) [NM_021065] | Member of the histoneH2A family | |
histone 1, H2bh (HIST1H2BH) [NM_003524] | Member of the histoneH2B family | |
histone 1, H2bd (HIST1H2BD) transcript variant 1, [NM_021063] | Member of the histoneH2B family | |
histone 1, H2bb (HIST1H2BB) [NM_021062] | Member of the histoneH2B family | |
histone 1, H3b (HIST1H3B) [NM_003537] | Member of the histoneH3 family | |
histone 1, H1e (HIST1H1E) [NM_005321] | Member of the histoneH1 family | |
immediate early response 3 (IER3), transcript variant short [NM_003897] | Protect cells from apoptosis | |
histone 1, H2bi (HIST1H2BI) [NM_003525] | Member of the histoneH2B family | |
major histocompatibility complex, class I, C (HLA-C) [NM_002117] | Operate in the immune system | |
major histocompatibility complex, class I, B (HLA-B) [NM_005514] | Operate in the immune system | |
major histocompatibility complex, class I, F (HLA-F) [NM_018950] | Operate in the immune system | |
histone 1, H4c (HIST1H4C) [NM_003542] | Member of the histoneH4 family | |
histone 1, H2bk (HIST1H2BK) [NM_080593] | Member of the histoneH2B family | |
histone 1, H2ae (HIST1H2AE) [NM_021052] | Member of the histoneH2A family | |
histone 1, H2bn (HIST1H2BN) [NM_003520] | Member of the histoneH2B family | |
histone 1, H2bl (HIST1H2BL) [NM_003519] | Member of the histoneH2B family | |
histone 1, H2bo (HIST1H2BO) [NM_003527] | Member of the histoneH2B family | |
histone 1, H2bj (HIST1H2BJ) [NM_021058] | Member of the histoneH2B family | |
histone 1, H2bm (HIST1H2BM) [NM_003521] | Member of the histoneH2B family | |
MCF7 | progastricsin (pepsinogen C) (PGC), transcript variant 1 [NM_002630] | * |
ets variant 7 (ETV7) [NM_016135] | Cellular processes on development and differentiation | |
proteasome (prosome, macropain) subunit, beta type, 8 [NM_004159] | Processing of class I MHC peptides | |
major histocompatibility complex, class II, DP beta 1 (HLA-DPB1), [NM_002121] | Operate in the immune system | |
transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) (TAP1), [NM_000593] | Multi-drug resistance | |
ubiquitin D (UBD) [NM_006398] | Many cellular processes | |
cDNA FLJ37399 fis, clone BRAMY2027587. [AK094718] | Tumor suppressor function | |
BE004814 MR2-BN0114-020500-006-e07 BN0114 H [BE004814] | * | |
cytidine monophosphate-N-acetylneuraminic acid hydroxylase [NR_002174] | * |
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Tsutsumi, K.; Masuda, M.; Date, H. Chromosomal Location of Genes Differentially Expressed in Tumor Cells Surviving High-Dose X-ray Irradiation: A Preliminary Study on Radio-Fragile Sites. Curr. Issues Mol. Biol. 2021, 43, 1133-1141. https://doi.org/10.3390/cimb43020080
Tsutsumi K, Masuda M, Date H. Chromosomal Location of Genes Differentially Expressed in Tumor Cells Surviving High-Dose X-ray Irradiation: A Preliminary Study on Radio-Fragile Sites. Current Issues in Molecular Biology. 2021; 43(2):1133-1141. https://doi.org/10.3390/cimb43020080
Chicago/Turabian StyleTsutsumi, Kaori, Moe Masuda, and Hiroyuki Date. 2021. "Chromosomal Location of Genes Differentially Expressed in Tumor Cells Surviving High-Dose X-ray Irradiation: A Preliminary Study on Radio-Fragile Sites" Current Issues in Molecular Biology 43, no. 2: 1133-1141. https://doi.org/10.3390/cimb43020080
APA StyleTsutsumi, K., Masuda, M., & Date, H. (2021). Chromosomal Location of Genes Differentially Expressed in Tumor Cells Surviving High-Dose X-ray Irradiation: A Preliminary Study on Radio-Fragile Sites. Current Issues in Molecular Biology, 43(2), 1133-1141. https://doi.org/10.3390/cimb43020080