Introduction
Bulk Methods to Assess ITH
Analysis of Tumor Biopsies From the Clinic
Sample / model | Methodology | |||||||
---|---|---|---|---|---|---|---|---|
Setting | Sample | Pros | Cons | Method type | ITH analyzed | Pros | Cons | Refs. |
Clinical | Tumor biopsies | • unmanipulated human biopsies • spatial sampling is possible | • difficulty in separating tumor and stroma • difficulty in obtaining numerous biopsies especially from rare breast cancer subtypes • difficult to obtain longitudinal samples at meaningful time points • biological replicates impossible • environment and genetic backgrounds are diverse • quality of sample is variable | Bulk profiling | • Genomic (DNA) | • relatively low cost • numerous computational methods available | • computational methods are estimations of true genomic architecture • the majority of genomic aberrations are passengers | |
• on-tissue (DNA, RNA, protein) | • spatial ITH discernable • correlations with morphological features • broad availability of clinical FFPE specimens | • limit of detection for low-abundance DNA or RNA targets • limited by availability of antibodies for proteins of interest | ||||||
Single-cell profiling | • Genomic (DNA) • transcriptomic (RNA) | • high resolution to more accurately model clonal architecture • ability to separate subpopulations based on profiles | • high cost • difficulty in obtaining sufficient cell numbers and high-quality cell samples | |||||
Liquid biopsies | • minimally invasive • ease of longitudinal biopsies • can encompass ITH from multiple disease sites | • may not capture all tumor cell subpopulations • small cell numbers obtainable • biological replicates impossible | Bulk profiling | • Genomic (DNA) | same as above | same as above | ||
Single-cell profiling | • Genomic (DNA) • transcriptomic (RNA) | same as above | same as above | |||||
Preclinical | GEMM | • possible to obtain biological replicates • fully intact immune system • native tumor-stroma interactions • controllable genetic manipulations/ reporters/ labeling • injectable models of metastasis | • non-human tumor cells • harbor less genomic complexity than human tumors • rapid timescale of tumorigenesis relative to human cancer • low rate of spontaneous metastasis • high cost and effort of mouse breeding • models for some breast cancer subtypes lacking | Bulk profiling | • Genomic (DNA) | same as above | cannot computationally eliminate stroma | [56] |
Single-cell profiling | • Transcriptomic (RNA) | same as above | cannot computationally eliminate stroma | |||||
Functional experiments | • CSC properties • inter-clonal cooperation • lineage tracing • intravital/ tissue imaging | • functional relevance beyond observational studies • dynamics observable through longitudinal studies • spatial ITH discernable on tissue • intravital imaging of in vivo cell behavior | • lengthy experimentation timelines • high cost of lentiviral libraries/sequencing/imaging | |||||
PDX | • possible to obtain biological replicates • human biopsy tumor cells • retain molecular complexity of human tumors • inter-patient heterogeneity represented among models • platform for preclinical trials • injectable models of metastasis | • lack of intact immune system • cross-species tumor-stroma interactions • selection of subclones can occur • high cost of immune-compromised mouse purchase and maintenance | Bulk profiling | • Genomic (DNA) | • ease of computationally discerning tumor from stroma | same as above | ||
Single-cell profiling | • Genomic (DNA) | • ease of computationally discerning tumor from stroma | same as above | |||||
Functional experiments | • CSC properties • lineage tracing • intravital/tissue imaging | same as above | • difficulty in generating long-term ex vivo cultures | |||||
Cell lines | • use of biological replicates • low cost • ease of genetic and functional manipulation • availability of injection models for xenograft studies | • lack of the full repertoire of ITH • in vitro-specific selection can occur • lack of microenvironment | Bulk profiling | • Genomic (DNA) | same as above | same as above | [84] | |
Single-cell profiling | • Genomic (DNA) • transcriptomic (RNA) • epigenetic (chromatin) | same as above | same as above | |||||
Functional experiments | • CSC properties • inter-clonal cooperation • lineage tracing | same as above | same as above |