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

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