Mutation and mutational signatures
Every cause of DNA damage leaves its own fingerprint. Sunlight, tobacco, a missing repair enzyme, even a gut bacterium, each write a recognisable pattern into the genome. Those patterns say what caused a cancer and which repair crews it lacks.
Diagram
Pick a product above a diagram to see the nodes it hits and the escape routes below the block. Hover or tap any node or arrow for what it is; every node opens its target, glossary entry or the pathway page. Violet boxes are druggable targets.
Footprints in snow. A fox, a dog and a child each leave a distinct print; you can tell who crossed the garden without having seen them. Cancer genomes are snowfields, and each mutagen and each broken repair crew leaves its own print.
What happens
In plain words, then the glossary entries the stage rests on. Chapter 2, How a cell becomes cancer: Cancer is evolution inside a body.
Every cause of DNA damage leaves its own fingerprint. Sunlight, tobacco, a missing repair enzyme, even a gut bacterium, each write a recognisable pattern into the genome. Those patterns say what caused a cancer and which repair crews it lacks.
Mutagenesis & mutational signatures. Every cause of DNA damage leaves its own fingerprint in the genome: sunlight, tobacco, a faulty repair enzyme, a gut bacterium. Reading these fingerprints tells you what caused a cancer and which repair crews it is missing, which in turn predicts which drugs will work.
The molecular players
The proteins and genes at this stage, with their role and how many products act on each. Listed players come from the atlas; drawn players sit as nodes in the diagrams above.
DNA repair genes. Inheriting a broken copy raises breast and ovarian cancer risk, but tumours that lose them become uniquely vulnerable to PARP inhibitors and platinum.
Where medicines act
Products grouped by the node they hit, most advanced first, with the cancers an approved product is linked to. Pick one above the diagram to see it light up.
- BRACAnalysis CDxApprovedOvarian cancerHR-positive / HER2-negative breast cancerTriple-negative breast cancer (TNBC)
- myChoice CDxApprovedOvarian cancer
- OlaparibApprovedOvarian cancerTriple-negative breast cancer (TNBC)HR-positive / HER2-negative breast cancer
- RucaparibApprovedOvarian cancerProstate cancerHigh-grade serous ovarian cancer
- TalazoparibApprovedTriple-negative breast cancer (TNBC)HR-positive / HER2-negative breast cancerProstate cancer
How tumours escape
Records tied to this stage that describe resistance, evasion or tolerance. The resistance atlas lists the routes class by class.
- preclinical evidenceresearchA standard evolvability score for every tumour
Some tumours change fast and escape drugs quickly; others are stable. A single validated score for how evolvable a tumour is would tell doctors how aggressively to combine treatments.
- preclinical evidenceindustrySlow the tumour's mutation engine with APOBEC inhibitors during targeted therapy
Subsets of lung, bladder and breast cancers carry raised APOBEC enzyme activity that keeps generating new mutations, feeding resistance. Blocking APOBEC3 alongside a targeted drug aims not to kill cells but to slow the rate at which resistant variants arise; the inhibitors are still in discovery.
- preclinical evidenceresearchTurn off the error-prone repair that manufactures resistance mutations
Under treatment stress, cancer cells switch on sloppy DNA copying that generates the mutations they need to survive. Blocking that machinery could stop resistance being invented.
- 2024rctNICHE-2: a month of nivolumab and ipilimumab before surgery clears mismatch-repair-deficient colon cancer in most patientsNew England Journal of Medicinechanged practice
- 2024translationalNICHE-2: a single dose of ipilimumab and two of nivolumab before surgery clears dMMR colon cancer in most patientsNew England Journal of Medicinechanged practice
- 2023translationalRojas 2023: a personalised mRNA vaccine trained T cells against each patient's pancreatic cancer, and those who responded stayed cancer-free longerNature
- 2018reviewRibas and Wolchok 2018: cancer immunotherapy using checkpoint blockadeScience
- 2018rctSOLO-1: two years of olaparib maintenance after first-line chemotherapy for BRCA-mutated ovarian cancerNew England Journal of Medicinechanged practice
Measured by
Biomarkers, tests and assays in the corpus that read this stage in a patient.
Open questions
What is not known at this stage: the atlas's own questions, the bottlenecks it bears on, and the ideas in the corpus that try to answer them.
- What causes the signatures with no known aetiology (a third of them)?
- Can signatures in blood detect exposure before cancer appears?
- being tested at scaleresearchA funded programme of organ-preservation trials to avoid radical surgery
For some cancers, drugs and radiotherapy can now cure without removing the organ, sparing patients a stoma, a lost voice or a removed bladder. A dedicated programme would run the trials to prove where this is safe.
- being tested at scaleclinicAutomatic germline testing for every cancer type where it changes care
Anyone with ovarian, pancreatic, metastatic prostate or mismatch-repair-deficient colorectal cancer should be tested for inherited mutations, yet testing rates fall well short. Making it an automatic, opt-out laboratory step triggered by pathology, as reflex mismatch-repair testing already is, would close the gap.
- being tested at scalepolicyEvaluate alcohol minimum unit pricing against cancer incidence
Scotland and Wales put a floor under the price of alcohol. Deaths from liver disease have already fallen. Cancer takes longer to show, so someone has to keep measuring for a decade.
- being tested at scaleclinicGet every Lynch syndrome carrier onto the right dose of aspirin
Aspirin roughly halves bowel cancer in Lynch syndrome, and a dose trial is defining how little is needed. Most carriers are still not prescribed it; the task is to fix prescribing.
- being tested at scaleMolecular-class-directed adjuvant therapy in endometrial cancer
Give adjuvant treatment by the tumour's molecular class rather than by stage and grade: nothing for POLE-mutated, immunotherapy for MMRd, chemotherapy plus targeted agents for p53-abnormal, hormones for NSMP.
- being tested at scaleclinicStanding reflex biomarker panels per tumour type, run without an oncologist's order
For each cancer type, agree the set of stains and tests that are always needed, and have the lab run them automatically on diagnosis rather than waiting for someone to ask.
- early clinicalresearchA frameshift neoantigen vaccine for Lynch syndrome carriers as the first preventive cancer vaccine approval
People with Lynch syndrome have a very high lifetime cancer risk from a predictable set of mutations. Vaccinate them against those shared mutations before cancer appears.
- early clinicalindustryA randomised trial of a shared-antigen vaccine to prevent Lynch syndrome cancers
Lynch syndrome tumours share predictable mutations the immune system can target. A vaccine in early trials could be tested to see if it prevents polyps and cancers in carriers.
- early clinicalindustryA single calibrated tumour mutational burden across all sequencing panels
Tumour mutational burden decides who gets immunotherapy in some settings, but every sequencing panel calculates it differently. A shared calibration would make the number mean the same thing everywhere.
- early clinicalMaking microsatellite-stable colorectal cancer immunotherapy-responsive
Ninety-five percent of bowel cancers ignore immunotherapy. Combinations that heat the tumour up (targeted drugs, radiation, new checkpoints) are the main hope.
7 more ideas are linked to this stage's pathways, targets and terms; see the rankings →
Key evidence
Papers in the corpus tied to this stage's pathways, targets and terms, newest first.
- 2024rctKEYNOTE-942: a personalised mRNA cancer vaccine plus pembrolizumab after melanoma surgeryThe Lancet
- 2024rctNICHE-2: a month of nivolumab and ipilimumab before surgery clears mismatch-repair-deficient colon cancer in most patientsNew England Journal of Medicinechanged practice
- 2024translationalNICHE-2: a single dose of ipilimumab and two of nivolumab before surgery clears dMMR colon cancer in most patientsNew England Journal of Medicinechanged practice
- 2023translationalRojas 2023: a personalised mRNA vaccine trained T cells against each patient's pancreatic cancer, and those who responded stayed cancer-free longerNature
- 2023rctRUBY: dostarlimab with chemotherapy for advanced or recurrent endometrial cancerNew England Journal of Medicinechanged practice
- 2022translationalCercek 2022: six months of dostarlimab alone made rectal cancer disappear in every patient with mismatch-repair deficiencyNew England Journal of Medicinechanged practice
- 2022rctDostarlimab alone cures mismatch-repair-deficient rectal cancer without surgery or radiotherapyNew England Journal of Medicinechanged practice
- 2021rctCheckMate 649: nivolumab plus chemotherapy as first treatment for advanced gastric, gastro-oesophageal junction and oesophageal adenocarcinomaThe Lancetchanged practice
- 2020rctCAPP2: two years of aspirin cuts bowel cancer in Lynch syndrome by more than a third over 10 yearsThe Lancetchanged practice
- 2020translationalFirst trial of a vaccine against the shared neoantigens of mismatch-repair-deficient cancersClinical Cancer Research
- 2020rctKEYNOTE-177: pembrolizumab instead of chemotherapy as first treatment for mismatch-repair-deficient metastatic colorectal cancerNew England Journal of Medicinechanged practice
- 2020observationalThe repertoire of mutational signatures in human cancerNature
src/data/mechanics-atlas.ts). Players, medicines, escape routes, tests, ideas and papers are resolved from the knowledge graph at build time through the stage's pathways, targets and terms, so every item here has its own page and sources. Where a section is missing, the corpus has no record tied to the stage yet. Nothing here is medical advice; see about and methodology. Stage 2.1 of 56.