Cancer arises from mutations in two key gene types: mutations leading to “loss-of-function” of the gene and mutations leading to a “gain-of-function”.
But this is only the beginning of the story. From disrupted tumor suppressors and hyperactive oncogenes, to large-scale chromosomal alterations, epigenetic drift, and environmental insults, cancer emerges through a convergence of events that dismantle the cellular safeguards.
Loss-of-Function Mutations: Tumor Suppressor Genes and Cancer
Tumor suppressor genes function as brakes, preventing uncontrolled cell division. When mutations inactivate these genes (through deletion, point mutations, or promoter disruptions), their protective role is lost. For instance, tumor suppressor genes like TP53 and RB1 are often inactivated early in cancer. TP53 loss removes key checkpoints for DNA repair and apoptosis, while RB1 inactivation disrupts the G1–S, unleashing uncontrolled proliferation.
Gain-of-Function Mutations: How Proto-Oncogenes Become Oncogenic
Proto-oncogenes on the other hand, act as accelerators of cell growth. When mutated, they become oncogenes, pushing cells to divide uncontrollably. Oncogenes such as KRAS and MYC gain function through mutations or amplification. KRAS mutations hyperactivate MAPK signaling, while MYC overexpression drives proliferation, metabolic rewiring to support rapid growth, and survival.
This imbalance, loss of tumor suppressor function, and gain of proto-oncogene activity lead to cancer, as cells lose regulatory control and proliferate unchecked.
Genetic Alterations-Copy Number Alterations (CNAs) and Chromosomal Instability in Cancer
CNAs and structural rearrangements, seen in most cancers, result from the gain or loss of genetic material from a few base pairs to an entire chromosome, often arise early and affect gene dosage by deleting tumor suppressors or amplifying oncogenes. A neuroblastoma model demonstrates that CNAs disrupt neural crest differentiation by promoting immature progenitor states. Combined with MYCN overexpression, they block normal development, induce tumorigenic traits, and rewire chromatin.
Epigenetic Changes That Drive Cancer and Increase Plasticity
Early epigenetic changes, such as hypermethylation of suppressor gene promoters or loss of chromatin repressors, induce repressive or overly permissive transcriptional states. This change allows cells to shift identity and evade regulation.
While the critical features of the epigenome have been largely studied, the drivers of epigenetic changes and the function of epigenetic regulatory genes during tumorigenesis have only recently been appreciated.
For instance, a recent study on lung cancer demonstrated how two major chromatin stability complexes, HBO1 and MLL1, normally help maintain lung cells’ identity and prevent them from dedifferentiating into immature cells. Disruption of either can undermine epigenetic control of tumor suppression.
Transcriptome Changes Analysis at the Single Cell Resolution
While scRNA-seq can’t directly analyze the genetic changes that initiate cancer, it is the most effective and comprehensive tool to analyze their downstream effects on each individual cell’s transcriptome.
When paired with computational methods, scRNA-seq data can be used to infer genomic changes like CNA and chromosomal instability, and be used to investigate tumor heterogeneity and evolutionary dynamics.
For instance, early childhood tumors begin with abnormal embryonic stem cells that carry large copy number alterations (CNA). In this paper, researchers analyzed human ESC differentiation with scRNA-seq and epigenome analysis to understand the link between CNA associated with neuroblastoma, consequent gene transcription amplification and tumor initiation. The authors discovered previously unknown genomic alterations and followed how they evolve over time. Cells with chromosomes 17 and 1 gain diverted from their normal fate into different lineages. MYCN gene gain of function locked the cells into proliferative, tumor-like states. By integrating scRNA-seq information with genomic analysis the authors could identify copy numbers and gain at the single cell resolution that revealed aberrant programs that underlie cancer development.
Ask a Single Cell
Decoding the Origin of Cancer with Single Cell Sequencing
The origins of cancer are rooted in genomic and epigenomic alterations that change cell phenotype and their dynamics within the tissue. By dissecting the molecular landscape of cancer cells, scRNA-seq is the tool to trace lineage hierarchies and uncover rare malignant subpopulations, or deconvolve clonal trajectories underlying early cancer cells.
By using scRNA-seq to premalignant and early tumor models, scRNA-seq can uncover transcriptional plasticity and the environmental cues that support the transformation.
Analyzing loss and gain of function in early stages of cancer
- How do loss-of-function or gain-of-function mutations reshape the transcriptional programs in early cancer cells?
- How does this transcriptional imbalance lead to lack of regulatory control and unchecked proliferation?
Genetic alterations and cancer.
- How CNA-driven subclones operate within the tumor ecosystem?
- How do structural rearrangements alter the developmental pathways? And how do they lead to cancer?
Epigenetic changes and tumor plasticity
- Does epigenetic reprogramming promote stem-like states conducive to tumorigenesis?
- What are the contributions of genetic and epigenetic alterations to a plastic state that can induce a fully transformed cell?
TLDR: Cancer does not appear all at once. It emerges through early genetic, chromosomal, and epigenetic disruptions that quietly alter how cells regulate growth, differentiation, and survival. Rather than producing a single outcome, these changes drive divergence in transcriptional programs across individual cells, laying the groundwork for heterogeneity and malignant potential. The earliest consequences of tumor initiation are written in gene expression, not DNA sequence alone. Single cell RNA sequencing reveals how these early alterations reshape transcriptional states across cells, bringing the first functional shifts of cancer development into view.
