Table 2.

Transcription factors (TFs) in BC pathogenesis studied in 3D culture.

Transcriptional Regulation of	TFs	Target Gene	Proposed Function in breast Carcinogenesis	Cell Lines Used for 3D Culture	Type of ECM	References
Mammary tissue architecture	P53	SREBP-1 and SREBP-2	Disruption of normal acinar morphology via mutant p53	MDA-468, MDA-231, and MCF10A	rBM matrix	[79]
	NF-κB	Disorganization genes	Disruption of tissue polarity and organization	HMT-3522 S1 and T4-2 cells	rBM matrix	[83]
	GATA3		Induces proliferation via mutant GATA3s	ZR751	Xenograft	[87]
	TAZ	IRS1	Induces proliferation	MCF10A	rBM matrix	[90]
	SOX7		SOX7 depletion causes loss of polarity and increased proliferation	MCF10A	rBM matrix	[93]
	TBX3		Branching morphology	MDA-MB-231	rBM matrix	[198]
	MRTF-A and MRTF-B	integrin α5, integrin α6	Disruption of normal acinar morphology	MCF10A	rBM matrix	[96]
	Sp1		Stiffness-induced tumorigenic phenotype and chromatin organization	MCF7 and MDA-MB-231	rBM matrix	[100]
EMT and metastasis	TWIST1	ADAM12	Induces tumor invasion and metastasis	Hs578T and HMLE cells	Matrigel–collagen mixture	[113]
	TWIST1	PRKD1	Promotes invasion, epithelial dissemination, and metastasis	murine and human mammary tumor tissues	Organoid	[116]
	SNAIL		SNAIL inhibition reduces invasion and metastasis	MCF7		[120]
	SNAIL		Downregulation of Snail induces a reversal of EMT in the bone	MDA-MB-231, mammary tumor cells, osteoblast-like cells	rBM matrix	[139]
	STAT3	LINC00520	Invasion and metastasis	MCF10A-Src transformed cells	rBM matrix, bioprinting	[121]
	STAT3		STAT3 inhibition blocks invasion	primary tumor tissue explant culture	rBM matrix	[122]
	∆Np63α		∆Np63α inhibition induces EMT	MCF10A	3D collagen gel	[126]
	OCT1-SOX2, PAX6-SOX2, OCT4-SOX2		aggressive cancer phenotype	T47D		[130]
	SP1, ZNF281, ZNF740, MZF1 and RREB1		aggressive cancer phenotype	T47D		[130]
	ZEB1	E- and N-cadherins	Induces EMT	HT1080	rBM matrix	[135]
	PROX1	MMP14	Inhibits invasion	MDA-MB-231	3D fibrin matrix	[127]
	JunB		EMT-induction	NMuMG and iLEC cells	3D co-culture fibrin beads	[140]
Apoptosis	NF-κB		Induced by tissue polarity and drives resistance to apoptosis	HMT-3522 sourced S-1 and T4-2 cells	rBM matrix	[56]
	RUNX2	Bcl-2 and IL-8	Disruption of normal acinar morphology, increased cell proliferation	MCF10A and MDA-MB-231	rBM matrix	[91]
	IRF6		Induced by detachment and downregulation causes anoikis resistance	MCF10A, HMEC	rBM matrix	[153]
Therapy resistance and drug response	HIF-1α	MDR-1	Increased resistance to doxorubicin	MCF7		[173]
	NF-κB	β1-integrin	Increased radioresistance	HMT-3522 S1 and T4-2 cells	rBM matrix	[176]
	MYC		Drives resistance to everolimus	MCF7, ZR75, CAMA-1	rBM matrix	[180]
	E2F1, ELK1, GATA, P53 and STAT4		Increased activity upon lapatinib treatment	MCF10A/ErbBB2	rBM matrix	[188]
	SREBP2	HMGCR and HMGCS1	Sensitizes to fluvastatin-induced apoptosis	MDA-MB-231 and MCF7	rBM matrix	[187]
Stemness	SOX2 and FOXO1		Accumulation of FOXO1 and enhanced SOX2 transcription supports BC stemness	Human breast cancer tissues	ULA plates	[193]
	NANOG and OCT4		Increased expression in mammospheres	MCF7 and SKBR3, and MDA-MB-231	Agar-coated plates	[199]
	SOX2, NANOG, OCT4, and FOXO3		Increased expression in cell surface-GPNMBhigh cells	BT-474, Hs578T, and MDA-MB-468	ULA or HEMA-coated plates	[201]