Table 2.
Top 20 most abundant altered genes and lncRNAs as effect of exposure to 12 serial doses of doxorubicin (P12), respectively 24 serial doses (p24) on both TNBC cell lines, Hs578T and MDA-MB-231
| Cell line | Analysis | RNA species | Upregulated | Downregulated |
|---|---|---|---|---|
| Hs578T | P12 versus P0 | Gene | FOS, FOSB, PCSK2, RCSD1, CXCL2, EGR1, SLC12A7, CXCL2, CXCL3, KIR2DS4, IL6, PKNOX2, IFITM1, CXCL8, SLC14A1, MX1, IFI27, IFITM1, DRD1, OAS1 | LCP1, HLA-DPB1, NCAM1, LPP, HAPLN2, WDR76, TRA2A, RHOJ, SH3GL3, ZBTB32, C3AR1, TAS2R30, CCDC177, PDE8B, FEM1A, CLDN10, KRT83, UTP11L, GALNT14, YIF1B |
| lncRNA | lnc-ARRDC3–1, C8orf4, lnc-AC092327.1–3, LINC01082, LINC01016, LOC152286, LOC100506474, C1orf167, LOC100133669, LOC101928093, FER1L4, LOC100240735, FENDRR, MRVI1-AS1, XLOC_l2_012847, CA5B, LINC01431, LOC100506098, lnc-EPSTI1–3, SNORD114–2 | TMEM200C, XLOC_l2_015885, RNA28S5, RNA18S5, lnc-CDKAL1–1, lnc-ANKRD53–1, TMPRSS4-AS1, lnc-C12orf49–2, SNRNP40, LOC441268, lnc-RASA1–3, LINC00271, LOC102031319, lnc-VPS4A-1, ZNF385D-AS2, lnc-TSC22D1–1, LOC100129940, lnc-CTBP1–1, HAAO, lnc-ANKRD11–2 | ||
| P24 versus P0 | Gene | FOS, FOSB, PCSK2, IDO1, SLC12A7, ATF3, EGR1, CXCL2, SLC14A1, DRD1, ATF3, RCSD1, BMP7, NR4A2, COLEC12, GABRA2, ACKR3, NR4A3, CES1 | LCP1, NAP1L3, NR0B1, NCAM1, HLA-DPB1, KRT83, FAM133A, NEFM, GALNT14, ST6GAL2, DOK5, MAGED4B, LMO7DN, SULT6B1, CILP, SH3GL3, EPB41L4A, SRD5A2, ITM2A, JPH1 | |
| lncRNA | CYP2S1, lnc-ARRDC3–1, lnc-AC092327.1–3, C8orf4, LINC01082, lnc-GABRA2–1, LUCAT1, CYP2S1, LOC101928093, lnc-EPSTI1–3, lnc-KLHDC10–2, FENDRR, lnc-ENPP2–1, CA5B, XLOC_l2_013293, LINC00524, LOC100506098, LOC344887, FENDRR, LOC101928582 | LOC100507377, SP3P, C16orf97, CAMK1D, LOC101928942, C1orf220, LINC01197, LOC101927115, lnc-CXCL2–1, lnc-MBP-1, LOC284009, lnc-AC078802.1–1, MCM3AP-AS1, lnc-RASA1–3, MKL2, lnc-PYDC2–1, lnc-ZNF91–2, HAAO, FLJ11710LOC100132495 | ||
| MDA-MB-231 | P12 versus P0 | Gene | CXCL2, CCL20, CSF3, FOSB, NR4A3, NR4A2, FOS, CSF2, LCN2, IL6, NPPB, ATF3, HES1, IL1A, CXCL1, CXCL3, C3, ATF3, SAA2, IL1B | THBS2, HTR1F, ATP8A1, SSX4B, SSX1, BEX5, POU3F2, SNCAIP, TIE1, SEPP1, SHISA3, PCSK5, PPP2R2C, DMD, CHRDL1, KLHL10, PELI2, CHRM2, ATP11AUN, CMKLR1 |
| lncRNA | RNA5-8S5, LOC729451, C1QTNF1-AS1, lnc-MTHFD2L-1, C4orf26, LOC102724910, LOC101928353, MALAT1, lnc-FLYWCH2–1, LINC00996, lnc-FGF9–1, C15orf48, lnc-ASMT-5, LOC101926959, XLOC_l2_015438, SAT1, lnc-DZIP1–3, NAMPT, HOXB-AS1, lnc-IL6–2 | lnc-IL1R2–1, lnc-POTEB-5, lnc-PRKD1–2, LOC643201, lnc-C14orf37–1, XLOC_l2_008221, SMEK3P, EPB41L4A-AS2, TMEM71, SSX8, XLOC_l2_012323, ZNF503-AS2, LOC101929484, lnc-RP1–177G6.2.1–2, TMEM92-AS1, lnc-GNLY-1, LOC101928710, LOC643201, lnc-MAFB-1, LOC101929395 | ||
| P24 versus P0 | Gene | FOSB, FOS, CXCL2, CCL20, IL6, CSF3, ATF3, NR4A3, NR4A2, NPPB, CXCL3, NKX2–1, LCN2, CSF2, EGR1, EGF4, HES1, C1QTNF1, ZFP36, MUC4 | THBS2, HTR1F, CHRDL1, ATP8A1, CMKLR1, SSX1, SSX4B, PCSK5, PAGE2B, PAGE2, POU3F2, PELI2, SEPP1, KIRREL3, COX7B2, TIE1, BEX5, KLHL10, GPR158, MMP1 | |
| lncRNA | XLOC_l2_012748, lnc-MTHFD2L-1, LOC729451, lnc-ME3–1, MALAT1, lnc-ASMT-5, C11orf53, lnc-FGF9–1, LOC102724910, C1QTNF1-AS1, lnc-ANKRD10–1, LOC101926940, SNORD36B, HOXB-AS1, LOC100133669, lnc-UMPS-2, LOC102724434, XLOC_l2_013125, XLOC_l2_015438, C11orf96 | lnc-POTEB-5, lnc-PRKD1–2, LOC101928942, XLOC_l2_012323, LOC643201, lnc-PTPRG-1, LINC01197, lnc-FOXL1–2, LOC101928915, LOC101928710, EPB41L4A-AS2, XLOC_l2_008783, LOC643201, SSX8, LOC100128242, LOC101928413, lnc-RP11-712 L6.5.1–2, lnc-BLID-1, lnc-CCDC140–5, lnc-JPH4–1 |