Heterogeneity
A biopsy samples one place at one time; the tumour is many places changing over time. Subclones with different drivers coexist, and the one that survives treatment was often a minority nobody sequenced.
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.
Clonal evolution is like weeding a field with one herbicide year after year: the field fills with the one weed that shrugs it off. Rotating herbicides and leaving some susceptible weeds to crowd out the resistant ones is the evolutionary alternative.
Chromosomal instability is a library that reshuffles and duplicates random shelves every night. Most rearrangements are useless, some ruin the building, but occasionally one yields a book the librarian needs to survive a new rule, and the mess itself keeps the fire alarms twitching.
The genome is the book; epigenetics is the highlighting and the pages stapled shut. Cancer staples shut the safety chapters and highlights the growth chapters. Epigenetic drugs pull staples.
What happens
In plain words, then the glossary entries the stage rests on. Chapter 9, Why treatments fail: Every cancer drug eventually meets resistance.
A biopsy samples one place at one time; the tumour is many places changing over time. Subclones with different drivers coexist, and the one that survives treatment was often a minority nobody sequenced.
Clonal evolution & minimal residual disease. A tumour is a population that evolves by natural selection. Treatment kills the sensitive cells and selects the rest, which is why resistance is the rule; measuring the surviving population (MRD) and adapting therapy is the counter-strategy.
Chromosomal instability & aneuploidy. Most cancers have the wrong number of chromosomes and keep shuffling them at every division. This chaos fuels evolution and drug resistance, but it also stresses the cell and can trigger immune alarms, a double edge that researchers are trying to exploit.
Epigenetic reprogramming. Cancer changes not just its genes but how they are read: chemical tags on DNA and histones silence guardians and awaken growth programmes. Unlike mutations, these changes are reversible, which is the hope behind epigenetic drugs.
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.
A growth receptor that is mutated in some lung cancers and overproduced in others; the first great success of targeted pills.
A metabolic enzyme whose mutant form produces a molecule that scrambles how genes are read; blocking it slows brain tumours and leukaemias.
TP53 is the 'guardian of the genome', broken in half of all cancers. Fixing it directly has so far defeated every attempt, so drugs exploit what its loss makes cancers depend on.
EZH2 is an enzyme that silences genes. The first drug against it treated a rare sarcoma and some lymphomas until it was withdrawn in 2026 for causing second blood cancers.
A scaffold protein that certain leukaemias need to keep their genes switched on; the first drug against it was approved in 2024.
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.
- AfatinibApprovedNon-small-cell lung cancerEGFR-mutated non-small-cell lung cancerHER2-mutant non-small-cell lung cancer
- AmivantamabApprovedNon-small-cell lung cancerEGFR-mutated non-small-cell lung cancerMET exon 14 and MET-amplified non-small-cell lung cancer
- AumolertinibApprovedNon-small-cell lung cancer
- CetuximabApprovedColorectal cancerHead and neck squamous cell carcinomaRecurrent or metastatic head and neck squamous cell carcinoma
- Cetuximab sarotalocanApprovedHead and neck squamous cell carcinoma
- cobas EGFR Mutation Test v2ApprovedNon-small-cell lung cancer
- DacomitinibApprovedNon-small-cell lung cancer
- EncorafenibApprovedColorectal cancerMelanomaNon-small-cell lung cancer
- +42 more at EGFR →
- EnasidenibApprovedAcute myeloid leukaemiaIDH1- and IDH2-mutated acute myeloid leukaemiaSinonasal undifferentiated carcinoma (SNUC) and SWI/SNF-deficient sinonasal carcinoma
- IvosidenibApprovedAcute myeloid leukaemiaBiliary tract cancer (cholangiocarcinoma)IDH1- and IDH2-mutated acute myeloid leukaemia
- OlutasidenibApprovedAcute myeloid leukaemiaIDH1- and IDH2-mutated acute myeloid leukaemia
- VorasidenibApprovedGlioma & glioblastomaAstrocytoma, IDH-mutant (grades 2 to 4)Oligodendroglioma, IDH-mutant and 1p/19q-codeleted
- HMPL-306Phase 3
- SafusidenibPhase 3
- TQB3454Phase 3
- SelinexorApprovedEndometrial cancerMultiple myelomaDiffuse large B-cell lymphoma
- OSE2101Phase 3
- KRT-232Phase 2
- EprenetapoptNegative
- MevrometostatPhase 3
- XNW5004Phase 2
- TazemetostatWithdrawn
How tumours escape
Records tied to this stage that describe resistance, evasion or tolerance. The resistance atlas lists the routes class by class.
- early clinicalresearchA multi-cancer platform trial of adaptive (dose-holiday) therapy
Instead of hitting a tumour with the maximum dose until it stops working, adjust the dose to keep the tumour small and let drug-sensitive cells suppress resistant ones. Test this properly across several cancers.
- early clinicalphilanthropyA national rapid research autopsy network for end-stage cancer
When patients who agreed in advance die of cancer, sampling every tumour within hours reveals how the disease evolved and escaped every drug. Few hospitals can do this today.
- early clinicalclinicBiopsy the one lesion that is growing while the others shrink
When a scan shows most tumours shrinking but one growing, that odd lesion holds the escape mechanism. Sampling it, and treating it locally, should be routine.
- early clinicalclinicPause a failed drug so the tumour becomes sensitive to it again
Resistant cancer cells can become dependent on the drug they resisted, as shown for BRAF-inhibitor-resistant melanoma in mice. Stopping the drug for a defined washout and then rechallenging, while tracking the resistance allele in blood tumour DNA, could make the tumour vulnerable to it once more.
- early clinicalengineeringUltrasound-assisted blood test instead of a brain biopsy
Brain tumours release little DNA into blood because of the blood-brain barrier. Sonobiopsy briefly opens the barrier with focused ultrasound and microbubbles, raising circulating tumour DNA severalfold so a blood sample can replace repeat surgical biopsy for diagnosis and resistance monitoring in glioma and brain metastases.
- early clinicalindustryVaccines aimed only at mutations shared by every tumour cell
Personal cancer vaccines target a list of mutations, some present in only part of the tumour, so the tumour can escape by losing them. Restricting vaccines and T-cell products to clonal mutations shared by every tumour cell, identified by multi-region sequencing, should close that escape route.
- 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 evidenceresearchAn open atlas of collateral sensitivity for every approved targeted drug
When a tumour evolves resistance to one drug, it sometimes becomes weaker against another. Map these trade-offs systematically so doctors can pick the next drug to exploit them.
- preclinical evidenceAttack extrachromosomal DNA, the engine of oncogene amplification
Aggressive glioblastomas, sarcomas and gastric cancers keep amplified cancer genes such as EGFR, MYC, MDM2 and CDK4 on free-floating DNA circles (ecDNA) whose copy number rises and falls quickly, letting the tumour dial resistance up and down. Cells carrying ecDNA depend on CHK1, giving a first drug target.
- preclinical evidenceresearchBarcode patient-derived tumours to watch which clones win under each drug
Tag every cell in a patient's lab-grown tumour with a unique DNA label, give it a drug, and read the labels to see which cells survive. This predicts which resistant clone will emerge.
- 2023observationalGALAXY: tumour DNA in blood four weeks after bowel cancer surgery predicts relapse tenfoldNature Medicine
- 2023translationalTRACERx 421: the full-cohort picture of how lung cancer evolves and which subclones drive relapseNature
- 2022reviewHallmarks of Cancer 2022: adding phenotypic plasticity, epigenetic reprogramming, microbiomes and senescent cellsCancer Discovery
- 2017reviewClonal Heterogeneity and Tumor Evolution: Past, Present, and the FutureCell
- 2017observationalIntegrating evolutionary dynamics into treatment of metastatic castrate-resistant prostate cancerNature Communications
- 2017translationalTRACERx first 100: tracking how lung cancers evolve, and how chromosomal chaos predicts relapseNew England Journal of Medicine
Measured by
Biomarkers, tests and assays in the corpus that read this stage in a patient.
- cobas EGFR Mutation Test v2PCR
- therascreen EGFR RGQ PCR KitPCR
- therascreen KRAS RGQ PCR KitPCR
- therascreen BRAF V600E RGQ PCR KitPCR
- FoundationOne CDxNGS tissue
- FoundationOne Liquid CDxNGS plasma
- Guardant360 CDxNGS plasma
- Oncomine Dx Target TestNGS tissue
- EGFR pharmDxIHC
- Abbott RealTime IDH1PCR
- Abbott RealTime IDH2PCR
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.
- How many regions or how much blood must be sampled to see the clones that matter?
- Can heterogeneity itself be reduced (anti-CIN drugs) to slow evolution?
- early clinicaldataA clone report from blood at every treatment cycle
Blood tests can already detect tumour DNA. Reporting which sub-populations of the tumour are growing or shrinking, cycle by cycle, would turn the test into an evolution monitor.
- early clinicalregulatorAn annual blinded shoot-out for liquid biopsy tests
Once a year, send the same blinded blood samples to every company selling a tumour-DNA test and publish how each performed.
- early clinicalregulatorCertified reference samples to benchmark every tumour-DNA blood test
Dozens of companies sell blood tests for tumour DNA and they report different results on the same sample. Government-issued reference samples with known amounts of tumour DNA would expose the differences.
- early clinicalresearchGroup trials by broken mechanism, not by organ or single mutation
Rare cancers often share a broken cellular machine even when they arise in different organs. Grouping patients by that shared fault makes trials possible.
- early clinicalIntercept cancer at the field stage
Whole regions of tissue carry cancer mutations long before a tumour exists. Detecting and treating the field, not the tumour, could prevent cancers rather than cure them.
- early clinicalIs aneuploidy itself a druggable vulnerability?
Most cancers have the wrong number of chromosomes; normal cells do not. If that difference creates a specific weakness, a drug against it would spare normal tissue by definition.
- early clinicaldataPush residual disease detection a hundredfold deeper with whole-genome methods
Current blood tests for leftover cancer track a few dozen mutations and miss low-level disease. Whole-genome and error-corrected methods integrate signal across thousands of tumour-specific sites plus methylation and fragment features, reaching detection near one part per million in research settings; cost, turnaround and reproducibility are the barriers.
- early clinicalpayerRe-test the metastasis, not the old primary, before every change of treatment
Treatment is often chosen from a biopsy taken years earlier from the original tumour. The spread disease may now look different. Test it again before switching drugs.
- early clinicalindustryTurn chromosomal chaos into a weakness with KIF18A inhibitors
Chromosomally unstable, often whole-genome-doubled tumours survive constant chromosome mistakes by depending on the motor protein KIF18A, which diploid cells do not need. Blocking it kills unstable cancer cells while sparing normal ones; inhibitors are in early trials in ovarian and other cancers.
- preclinical evidenceresearchAn open model of every cancer cell state, built from perturbation atlases
Map every state a cancer cell can be in, and how drugs and the surrounding tissue move it between states, into an open computational model anyone can query and improve.
22 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.
- 2023observationalGALAXY: tumour DNA in blood four weeks after bowel cancer surgery predicts relapse tenfoldNature Medicine
- 2023translationalTRACERx 421: the full-cohort picture of how lung cancer evolves and which subclones drive relapseNature
- 2022reviewHallmarks of Cancer 2022: adding phenotypic plasticity, epigenetic reprogramming, microbiomes and senescent cellsCancer Discovery
- 2018observationalChromosomal instability drives metastasis through a cytosolic DNA responseNature
- 2018observationalGenome doubling shapes the evolution and prognosis of advanced cancersNature Genetics
- 2018basicTCGA Pan-Cancer Atlas: 10,000 tumours across 33 cancer types, classified by molecular featuresCell
- 2017reviewClonal Heterogeneity and Tumor Evolution: Past, Present, and the FutureCell
- 2017observationalIntegrating evolutionary dynamics into treatment of metastatic castrate-resistant prostate cancerNature Communications
- 2017reviewStandards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American PathologistsThe Journal of molecular diagnostics
- 2017translationalTRACERx first 100: tracking how lung cancers evolve, and how chromosomal chaos predicts relapseNew England Journal of Medicine
- 2016reviewEpigenetic Determinants of CancerCold Spring Harbor perspectives in biology
- 2015basicMartincorena: normal sun-exposed skin is a patchwork of cancer-mutation clonesScience
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 9.2 of 56.