Table 1.

Comparison of the advantages and disadvantages of 2D culture systems vs. 3D mono-culture, co-culture, and 3D chamber systems relevant to breast cancer [18, 22, 56–7,3]

Model system	Benefits	Limitations
2D monoculture	• Relatively fast data acquisition [61] • Cost effective • Discover new mechanisms and pathways in cells • Provides a controlled environment • Can perform certain types of experiments (e.g., cellular  fractionation, pull-downs) • Can be applied to high-throughput applications	• No interactions between cells and the ECM  or other aspects of the tissue microenvironment [63, 74] • Not necessarily reflective of patients
3D culture in synthetic matrix (e.g., agarose)	• Discover new mechanisms and pathways in cells • Provides a controlled environment • Scalable to different plate format • Can be applied to high-throughput applications • Can also accommodate co-culture techniques • Can study impact of microenvironment [64] • Can mine for genetic drivers in malignant progression [18] • Can simulate physical environment [65]	• Acquisition of data takes time [66] • Can be expensive • May require specialized devices and software • Limits techniques due to the presence of matrix • Long-term culture is difficult to achieve • Difficult to apply to high-throughput applications
3D rBM monoculture	• More accurately represents gene [67]  and protein expression [68], as well as drug [60, 68]  and radiation response [69] than 2D culture • Better recapitulates changes in cellular polarity [70],  responses to environmental cues [22],  and presents a more accurate cell signalling profile [71]  than 2D culture or synthetic matrices. • Facilitates study and characterization of proteases involved  in ECM remodeling [56, 72]	• Acquisition of data takes time • Expensive • Limits techniques due to the presence of matrix • Matrix may differ from lot to lot  (leading to inconsistencies in cell behavior) • Long-term culture is difficult to achieve • Difficult to apply to high-throughput applications
3D rBM co-culture	• Incorporates multiple cell types present  in the microenvironment such as fibroblasts [57]  and myoepithelial cells [58]  for a more accurate depiction of tissue niche • Direct and indirect methods can elucidate  the need for physical cellular interation	• Acquisition of data takes time • Expensive • Limits techniques due to the presence of matrix • Matrix may differ from lot to lot  (leading to inconsistencies in cell behavior) • Long-term culture is difficult to achieve • Multiple cell types need to be distinguishable from one another  (e.g., fluorescent tags for microscopy) • Difficult to apply to high-througput applications • Ratio of cell types plays a role in the outcome
3D chamber sytems	• Facilitates analysis over long periods of time [73] • Facilitates investigation of environmental factors of the  invasion of ductal carcinoma [59]	• Acquisition of data takes time • Expensive • Limits techniques due to the presence of matrix • Requires specialized devices • Difficult to apply to high-throughput applications