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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

From: New insights in gene expression alteration as effect of doxorubicin drug resistance in triple negative breast cancer cells

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