Introduction
Different levels of heterogeneity
Biomarkers
Metabolism
Cell cycle
TME
EMT, CSCs, and CTCs
Microcirculation
Clinical pathology
Breast cancer heterogeneity affects disease progression
Therapeutic resistance
Recurrence and metastasis
Cell interactions contribute to breast cancer heterogeneity
Breast cancer cells—fibroblasts
Breast cancer cells—adipocytes
Breast cancer cells—immune/inflammatory cells
Breast cancer cells—normal epithelial cells
Breast cancer cells—breast cancer cells
Research methods to measure heterogeneity
Measuring heterogeneity in mixed cellular populations
Measuring heterogeneity in single cells
Measuring heterogeneity in tissue slices preserving spatial information
Measuring heterogeneity in patients through medical imaging
State of sample | Application | Example | Advantages | Disadvantages | Refs. |
---|---|---|---|---|---|
Mixed cellular populations | At genomic and transcriptomic levels | Sanger sequencing | High accuracy | Laborious, expensive, lack of single-cell information and spatial information | [195] |
At the epigenomic level | NOMe–seq | Single-molecule real-time sequencing | Limited by the incompleteness of the human genome reference, with large gaps persisting in highly repetitive areas | [196] | |
At the proteomic level | Chromatography-based techniques, ELISA, western blotting, protein microarray, gel-based approaches | Identification of biomolecules using inherent properties, sequence of molecules, electrical charge | High effects of low quality and/or quantity of biomolecules. Limited in identification of rare peptides | ||
MS | Label-free. High throughput. Identification of posttranslational modifications | High complexity of analysis. Limited in identification of rare peptides | |||
Edman sequencing | Useful for the elucidation of residue deletions, the presence of common stable derivatives, and for following the progress of the synthesis itself | Limited in quantitation and the type and degree of adduct formation | |||
Single cells | At the genomic level | HM-SNS | Preserving single-cell information. High throughput | Loss of spatial information | |
Modular single CTC analysis pipeline | Each step is adjustable. Preserving single-cell information | Loss of spatial information | [60] | ||
At the epigenomic level | scATAC-seq | Preserving single-cell information | Loss of spatial information | [10] | |
scDNase-seq | Preserving single-cell information | Loss of spatial information | [11] | ||
scNOMe–seq | Preserving single-cell information | Loss of spatial information | [12] | ||
scChIP-seq | Preserving single-cell information. High throughput | Chip design is highly complex. Loss of spatial information | [202] | ||
At the transcriptomic level | scRNA-seq | Preserving single-cell information | Loss of spatial information | ||
At the proteomic level | OFCM | Preserving single-cell information. Counting in real time | Loss of spatial information. Chip design is highly complex | [210] | |
LC-Q-TOF-MS/MS | Preserving single-cell information | Loss of spatial information | |||
Tissue slices | At the genomic level | TSCS | Preserving single-cell information. Preserving spatial information | High complexity in use | [213] |
At the epigenomic level | SNuBar-ATAC | Preserving single-cell information. Preserving spatial information. Highly accurate. Easy to use. High throughput | Loss of partial sequencing reads. Mapping rate is not very high | [214] | |
At the transcriptomic level | FluoELs | Preserving single-cell information. Preserving spatial information. Error-correcting capability. Low cytotoxicity | Low throughput | [216] | |
CITE-seq | Preserving single-cell information. Preserving spatial information | Loss of information of some cell types | [19] | ||
At the proteomic level | MIBI-TOF | Preserving single-cell information. Preserving spatial information. Allow to revisit a sample after prolonged periods of time | [217] | ||
IMC | Preserving single-cell information. Preserving spatial information | Antibodies are not commercially available | |||
Organs/patients | Mammography, US, and MRI | Relatively effective and widely adapted in hospitals | Excessive cost. Harmful radiation. Lacks sensibility. Inconvenience to the patients | [224] | |
PET, SPECT | Effective in detection of metabolism and metastasis | Anatomical details are lacking | [225] | ||
Radiomics | Contain first-, second-, and higher-order statistics. Possibility of data sharing. Ability of quantitation | Difficulty in reproducibility | [228] |