Tumour Heterogeneity and Cancer Genomics

Overview of Tumour Heterogeneity

• Genetic Variation in Cancer: The genetic characteristics of cancers exhibit significant variability across three primary dimensions:

  • Between Patients: Variability in the genetic profile of the same cancer type across different individuals.

  • Between Tumours in a Single Patient: Differences between the primary tumour and metastatic sites.

  • Between Individual Cells: Variation among the specific cells within a single tumour mass.

• Levels of Heterogeneity Defined (Mariam Jamal-Hanjani et al., 2015):

  • Interpatient Heterogeneity: The occurrence of unique subclones within the tumours of different patients.

  • Intratumor Heterogeneity: The presence of multiple distinct subclones within a single primary tumour, leading to diverse characteristics among individual tumour cells.

  • Intermetastatic Heterogeneity: Differences between individual metastatic lesions in the same patient. This arises because some subclones may be derived directly from the primary tumour, while others emerge due to acquired alterations within the specific metastatic site.

  • Intrametastatic Heterogeneity: The presence of multiple subclones within a singular metastatic lesion.

Biological and Structural Components of Tumour Heterogeneity

• Composition of the Tumour Microenvironment: A tumour is not a homogenous mass of identical cells; it includes:

  • Infiltrating T-cells: These cells act against tumour neo-antigens that are recognized as "non-self."

  • Infiltrating Stromal Cells: Examples include cancer-associated fibroblasts that support the tumour.

  • Blood Vessels: Necessary for nutrient delivery and waste removal.

• Selection Pressures and Progression:

  • Selection Pressures: External factors like chemotherapy act on the tumour population.

  • Subclone Sensitivity: Some subclones are sensitive to selection pressures and are killed.

  • Intrinsic Resistance: Some subclones possess inherent resistance allowing them to survive treatment.

  • Acquired Alterations: New mutations can emerge that promote cell survival and proliferation, leading to an outgrowth of resistant populations in metastatic sites like the brain or liver.

• Case Study Data (Colorectal Cancer): Analysis of a cohort containing over 700 colorectal cancer patients shows heterogeneity at the cell signaling level. Individual biopsies typically contain between $2,000$ and $5,000$ cells.

Intra-tumour Variation and Evolutionary Mapping

• Evolutionary Phylogenetic Trees: Researchers use phylogenetic models to trace the lineage of mutations within a tumour mass.

  • Truncal Mutations: These are mutations present in all cancer cells, occurring early in the tumour's development (the "trunk" of the tree).

  • Subclonal Mutations: These occur later in the development process and are only present in a subset of the tumour cells (the "branches").

• Impact of Chemotherapy on Clonal Composition:

  • At initial diagnosis, a tumour may have a specific clonal fraction.

  • During the "Best Response" phase of treatment, certain subclones may be depleted.

  • During "Progressive Disease" (measured by RECIST criteria), resistant subclonal mutations often lead to the regrowth of the tumour mass.

• TRACERx Study Findings (Jamal-Hanjani et al., 2017):

  • The study analyzed 100 patients: Patients 1–61 (Adenocarcinoma), 62–93 (Squamous-Cell Carcinoma), and 94–100 (Other).

  • Disease-free Survival (DFS) and Subclonal Mutations: There was no statistically significant difference in DFS based purely on the percentage of subclonal mutations ($Hazard Ratio = 0.86$, $P = 0.70$).

  • DFS and Copy-Number Alterations: A high percentage of subclonal copy-number alterations was strongly associated with a higher risk of recurrence or death ($Hazard Ratio = 4.9$, $P = 4.4 \times 10^{-4}$).

Bases and Levels of Heterogeneity

• Bases of Heterogeneity:

  • Genome: Occurs via point mutations, Single Nucleotide Variants (SNVs), insertions, deletions, amplifications, allelic losses (Loss of Heterozygosity or LOH), and karyotype aberrations.

  • Transcriptome/Proteome: Defined by different patterns of gene expression or the over-/under-expression of specific genes within different subclones. This profile typically mirrors the genomic/epigenomic heterogeneity.

  • Epigenome: Defined by varying patterns of DNA methylation and noncoding RNA regulation, as well as differences in chromatin and histone structure.

• Hierarchical Levels:

  • Interpatient: Differences between individual patients' primary tumours.

  • Intertumor: Differences between a primary tumour and its metastases, or between two different metastatic lesions.

  • Intratumor: Diverse subclones within the primary tumour itself.

Models of Tumour Heterogeneity

• Cancer Stem Cell (CSC) Model:

  • Definition: This model asserts that only a small, rare subset of cells within a tumour is actually tumorigenic (capable of forming new tumours).

  • Properties of CSCs: These cells have the ability to self-renew and give rise to a phenotypically diverse population of progeny.

  • Comparison to Normal Stem Cells: Normal stem cells are rare cells in tissue that drive organogenesis via self-renewal and differentiation; CSCs are their malignant counterparts that drive tumorigenesis.

  • Origin: CSCs may arise from mutations in normal adult stem cells or progenitor cells that gain self-renewal capabilities.

  • Progeny: The offspring of CSCs are generally not self-renewing and are genetically similar to the CSC but lack the power to drive the tumour independently.

• Clonal Evolution Model:

  • Definition: Tumours arise from a single mutated cell and accumulate mutations over time.

  • Progression: As the tumour progresses, additional mutations create new subpopulations. Each subpopulation retains the ability to divide and mutate further.

  • Selection: Mutations that provide a growth advantage (e.g., resistance to apoptosis) allow certain lines to dominate. This process can eventually grant "stem-cell-like" properties to certain subsets of cells.

• Integrated Model: The contemporary view of tumour heterogeneity combines the Cancer Stem Cell hypothesis, the Clonal Evolution model, and the role of the tumour microenvironment.

Models of the Metastatic Process

• Clonal Selection Model: Suggests that only specific subclonal populations that already possess all the necessary prerequisites for metastasis are the ones that actually metastasize.

• Parallel Evolution Model: Proposes that metastasis occurs very early in the tumour's progression and that the metastatic lesion evolves independently from the tumour cells at the primary site.

• Dynamic Heterogeneity Model: Suggests that the metastatic potential of a primary tumour is determined by the frequency at which metastatic variants arise. In this model, cells in metastatic foci may eventually lose their metastatic properties.

• Clonal Dominance Model: Proposes that specific metastatic subclones within the primary tumour outgrow all other cells, eventually dominating both the primary tumour mass and the metastatic sites.

• Stem Cell Model of Metastasis: Asserts that only the cancer stem cells, rather than the bulk of the tumour cells, have the capacity to migrate and form new tumours at distant sites.

Therapeutic Implications

• Treatment Failure: Most current therapies fail because they target rapidly proliferating non-tumorigenic progeny cells while sparing the relatively quiescent cancer stem cells.

  • Targeting Rapidly Dividing Cells: This kills the bulk of the tumour but leaves the "roots" (CSCs) intact.

  • Targeting Cancer Stem Cells: Effective therapies must specifically identify and kill the cancer stem cells or "stem-like" cells to prevent recurrence and metastasis.

• Monitoring Heterogeneity: Understanding the presence of subclonal mutations and copy-number alterations is critical for predicting patient prognosis (e.g., higher risk of death with high subclonal copy-number changes).