Abstract Management of multiple primary tumours is an increasing clinical burden as the population of cancer survivors rises globally. Despite standard-of-care histological, radiological and panel sequencing diagnostics, identifying multiple primary cancers remains clinically challenging. We characterize multiple primary tumours in the TRACERx study. We integrate baseline and follow up clinical data, centrally-reviewed histopathological assessments with whole-exome sequencing (WES) to identify patients with multiple primary tumours from lung and other sites. Where multi-region sample collection was available, we assessed the genomic relatedness of multiple lesions from the same patient through shared clonal mutations. 205 (24% of 844) TRACERx patients had clinically-diagnosed or genomically-discovered multiple primary cancers. Of these, 82 patients had a prior cancer diagnosis, 56 patients had synchronous primaries at study enrollment, and 95 developed new primaries during follow up. Lung was the most common organ site for additional primaries, with 98 patients having two or more lung primary tumours, including the lung tumour profiled for the TRACERx study. High resolution tumour WES revealed clinical misclassification in 21 of 138 patients (15.2%) with multiple sequenced lesions. At baseline, clinical classification favoured relatedness between lesions: two patients diagnosed with intrapulmonary metastases actually had independent primary lung cancers. In addition, eight patients with lesions staged histopathologically as single tumours, some with microscopic evidence of histological heterogeneity, were confirmed through WES to be collision tumours composed of 2 to 3 independent lineages. One patient was discovered to have had synchronous lung primaries, undetectable clinically, through WES sequencing of lymph node metastases. During follow up, clinical classification tended to favour independent primary designation, with 6 of 10 discrepancies due to clinically-diagnosed metachronous primary tumours found through WES to be metastases. Together, the TRACERx multiple primary cohort represents one of the largest multi-region cohorts of multiple primary lung cancers analyzed to date. These data demonstrate the clinical utility of WES in diagnosing independent primary cancers. Ongoing analysis will investigate the association between history of multiple primary cancers and germline cancer susceptibility and patient outcome. Deep, multi-region molecular characterization, available for 58 patients with multiple primary lung cancers, will also allow detailed exploration of the molecular mechanisms driving the evolution of multiple primary cancers, informing potential biomarkers to highlight patients with elevated risk of secondary primary tumours and improve subsequent clinical management. Citation Format: Lydia Y. Liu, Charlotte Grieco, Adriana Salcedo, Takahiro Karasaki, Cristina Naceur-Lombardelli, Oliver Shutkever, Ariana Huebner, Carlos Martinez Ruiz, Sara Waise, Aino-Maija Leppä, Olivia Lucas, Tej Pandya, Selvaraju Veeriah, Sophia Ward, Kerstin Haase, Alexander A. Azizi, Woody Z. Zhang, Emma Hazelwood, Alexandar M. Frankell, TRACERx Consortium, Allan Hackshaw, Nicholas McGranahan, David A. Moore, Mariam Jamal-Hanjani, Charles Swanton. Clinico-genomic characteristics of multiple primary cancers in TRACERx [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 6793.

Limited understanding of the biological processes that govern metastatic dissemination hinders its prevention and treatment1. Here, using 501 longitudinally collected primary and metastatic tumour samples from 24 patients with non-small cell lung cancer (NSCLC) enrolled in the TRACERx lung study and PEACE autopsy programme, we infer tumour evolution from diagnosis to death. With DNA-sequencing data encompassing 70% of the metastases that were radiologically detected before death and paired multi-region sampled primary tumours, we show that the genomes of metastases diverge markedly from those of their ancestral primary tumour, with additional driver alterations and genome doubling events occurring after metastatic dissemination. In 62.5% of patients, multiple primary tumour subclones disseminated, each founding a distinct metastasis. These metastases served as sources of onward spread: more than half of the metastases sampled were seeded by other metastases. The duration that metastases existed in situ influenced their likelihood of seeding further metastases. Most metastatic migrations started and ended in the same anatomical cavity. The few subclones that exited the thorax to seed metastases disseminated widely and were enriched for somatic copy-number alterations, suggesting that chromosomal instability may facilitate extrathoracic spread. This spatial and temporal evolutionary analysis sheds light on the extent of metastatic diversity and seeding in advanced NSCLC-which tends to be underestimated in single metastasis biopsies-and identifies genomic and clinical mediators of metastatic progression.

Abstract Understanding the spatial and temporal dynamics of tumour evolution is crucial for determining the drivers of cancer progression. Linking genotype to phenotype across a tumour remains challenging, however. Here, we use single-cell and spatial multi-omics to comprehensively profile a primary malignant peripheral nerve sheath tumour (MPNST) and its multifocal recurrence. Combining the native barcoding system from extensive heterogeneity in copy number alterations with mutation data, we resolve the evolutionary tree of this tumour, revealing a branching structure suggestive of ongoing chromosomal instability. We show that gene dosage effects contribute to phenotypic diversity and scale predominantly linearly with copy number. Using spatial genomics assisted by laser capture microdissection and spatial transcriptomics, we performed in situ lineage tracing in this human tumour, elucidating the relationship between local expansions and interactions between tumour cells and the microenvironment. These findings demonstrate the potential of combined bulk, single-cell and spatial techniques to dissect cancer evolution in time and space and link genotype to phenotype in detail.

ABSTRACT Background Clinician-scientists translate clinical observation into discovery, trials, and policy, yet this workforce is shrinking across health systems worldwide. Integrated MB-PhD training, pausing medical training to complete a PhD before clinical exposure or specialisation, is one route into this career. We aimed to evaluate the long-term value of MB-PhD training and the barriers to clinical-academic careers faced after graduation. Methods We evaluated all 131 graduates (29.8% female) who entered the University College London (UCL) MB-PhD programme over a 25-year period (1994-2018). Bibliometric outputs were collated via an inter-linked information system. Concurrently, all 131 graduates were invited to respond to open-ended questions on career benefits and structural barriers; 99 (75.6%) responded, and responses were independently coded into themes, which were then reviewed and confirmed by a Study Group of 107 individuals, including the 91 respondents who agreed to participate further. Results Graduates produced 5,877 publications (1,141 first-author, 819 corresponding-author), attracting 350,754 citations, with a mean relative citation ratio of 3.30 ± 0.47, approximately three times the field average and sustained across three decades of programme entry. Graduates secured an estimated $157.55 million across 99 grants, released 465 public datasets, and were named investigators on 31 clinical trials across five continents. Among the 99 survey respondents, 49.5% held consultant-grade posts, 72.7% remained research-active, and 25.3% had reached senior academic grade. Openended responses were coded into five recurring structural barriers, subsequently confirmed by the Study Group: insufficient protected research time (72.2% of responses), unsupportive training structures and limited career opportunities (36.7%, 24.4% of responses), funding and pay barriers (22.2% of responses), and lack of mentorship or geographical/family constraints (14.4%, 13.3% of responses). Conclusions Integrated MB-PhD training generates sustained academic productivity and leadership, but structural barriers threaten retention of graduates within clinical-academic careers. Protecting research time, stabilising funding and pay, and reducing geographic instability, amongst other interventions, are needed to retain the clinician-scientists that health systems have already invested in training.

Tumors evolve through a process of selection on somatic mutations, driving cell division and tissue growth through aberrations in cell-cycle control. In non-small-cell lung cancer (NSCLC), genome instability occurs early in tumor growth, resulting in pronounced intratumor heterogeneity, including changes in gene copy number, and whole-genome doubling (WGD) in ∼75% of tumors. Gene duplication, genetic drift, and selection mediate functional diversification during evolution. In this study, we seek to identify the diversification and potential gene neofunctionalization of lung tumors in the TRACERx cohort. We develop a novel computational protocol to identify preduplication and postduplication mutations predicted to affect protein function. Mutations are analyzed using paralogs grouped into functional families with highly similar functions, identifying 355 functional impact events (FIEs) through their proximity and clustering near to functional sites. The use of functional family paralogs to map mutations to protein structures from the PDB helps predict putative rare driver events in lung tumors. By extending the analysis with high-quality structural models from AlphaFold using The Encyclopedia of Domains (TED), we find a significant increase in the diversity of both genes and functional families with postduplication FIEs in lung adenocarcinomas, including some metabolic enzymes with the potential to be neofunctional. The postduplication diversification of driver genes and functions may indicate selection for somatic copy number changes in lung tumors and an increased scope for tumor adaptations.

DNA mutations are a well-characterized source of neoepitopes in immunotherapy. Here, we examined the contribution of dysregulated RNA processing to neoantigen production. Leveraging multi-omics and checkpoint inhibitor (CPI) response data from >1,000 patients, we identified reduced activity of the nonsense-mediated mRNA decay (NMD) pathway kinase SMG1 as a predictor of improved CPI response. NMD inhibition through SMG1 targeting stabilized transcripts containing premature termination codons, most of which were of non-mutational origin. This reshaped the major histocompatibility complex class I (MHC class I)-bound immunopeptidome and increased neoantigen abundance to levels comparable to high mutation burden tumors. Functionally, NMD inhibition drove antigen-dependent T cell-mediated tumor cell killing in vitro, promoted activation of tissue-resident T cells in patient-derived models ex vivo, and improved CPI efficacy in vivo. Our findings establish NMD inhibition as a strategy to harness a previously inaccessible source of canonical and non-canonical neoantigens, with the potential to increase tumor immunogenicity across cancers.

Lung cancer remains the leading cause of cancer-related deaths worldwide, partly because many patients are diagnosed at late stages, highlighting the urgent need for effective early detection and intervention strategies. Low-dose computed tomography (LDCT)-based screening reduces lung cancer mortality in high-risk populations defined by age and smoking history; however, the uptake of LDCT remains low among eligible individuals. Compounding this issue, modelling studies estimate that nearly half of lung cancers occur in individuals who do not meet eligibility criteria for LDCT-based lung cancer screening under current guidelines. Moreover, LDCT-based screening has inherent limitations, including a high rate of false-positive results that can lead to unnecessary invasive procedures, as well as substantial costs that limit scalability. Major efforts have been made to identify novel biomarkers such as radiomic features and liquid biopsy assays to enhance the accuracy of lung cancer risk prediction. Furthermore, the increasing detection of pulmonary nodules by LDCT or diagnostic CT scans has highlighted the importance of therapeutic interventions that can enable interception of high-risk precancerous nodules and halt their progression to invasive disease. In this Review, we summarize the current state of lung cancer screening, the disparities and infrastructural considerations for optimal implementation, and future directions in the development of biomarkers and design of precancer interception strategies that could transform both lung cancer prevention and early intervention.

Cancers rarely respond completely to immunotherapy. While tumors consist of multiple genetically distinct clones, whether this affects the potential for immune escape remains unclear due to an inability to isolate and propagate individual subclones from human cancers. Here, we leverage the multi-region TRACERx lung cancer evolution study to generate a patient-derived organoid - T cell co-culture platform that allows the functional analysis of subclonal immune escape at single clone resolution. We establish organoid lines from 11 separate tumor regions from three patients, followed by isolation of 81 individual clonal sublines. Co-culture with tumor infiltrating lymphocytes (TIL) or natural killer (NK) cells reveals cancer-intrinsic and subclonal immune escape in all 3 patients. Immune evading subclones represent genetically distinct lineages with a unique evolutionary history. This indicates that immune evading and non-evading subclones can be isolated from the same tumor, suggesting that subclonal tumor evolution directly affects immune escape.

Abstract Background: Sensitive and scalable detection of circulating tumour DNA (ctDNA) is essential for minimal residual disease (MRD) assessment following curative-intent treatment in non-small cell lung cancer (NSCLC). While personalised, tumour-guided approaches are highly sensitive, they typically rely on bespoke panel design, limiting scalability and constraining the breadth of biological signals that can be interrogated. Error-corrected whole-genome sequencing (WGS) offers the potential to overcome these limitations by enabling personalised MRD detection without custom sequencing panels, while supporting genome-wide and tumour-agnostic analyses. Methods: We analysed personalised WGS-based ctDNA detection using Ultima Genomics’ ppmSeq in a TRACERx pilot cohort comprising 45 post-operative plasma samples from individuals with early-stage NSCLC during the landmark period. Landmark was previously defined as between days 10 and 120 post-operatively, prior to the start of adjuvant therapy or disease recurrence. Tumour-specific variants derived from tumour WGS were queried in genome-wide matched plasma. Plasma WGS was performed to a target coverage of 150x. Analytical sensitivity, ctDNA fraction distributions, and associations with relapse-free survival were assessed. Results: Error-corrected WGS enabled detection of tumour-informed variants at parts per million (ppm) allele fractions without bespoke panel design. Among MRD-positive samples, 13% exhibited ctDNA fractions below 10 ppm, and 72% were below 100 ppm, highlighting sensitivity across the ultra-low ctDNA range. The lowest ctDNA fraction called was 2.2 ppm. Landmark ctDNA detection by WGS was significantly associated with relapse-free survival, with a median relapse-free survival of 23.2 months in landmark-positive individuals (n = 37) compared with 98.7 months in landmark-negative individuals (n = 8, log-rank p = 0.042). Conclusions: These data provide early validation of personalised, tumour-guided ppmSeq ctDNA detection in early-stage NSCLC, with ctDNA quantification to parts per million. This approach is now being expanded to include up to 400 individuals from TRACERx (>1,500 plasma timepoints) to evaluate prognostic performance and scalability, positioning plasma WGS as a next-generation MRD platform that unifies personalised and tumour-agnostic monitoring from a single assay, including genome-wide error-corrected mutations, copy number, and fragmentation features for residual disease and relapse monitoring. Citation Format: Jonathan Wan, Sophie Ward, Alexander Azizi, Hila Benjamin, Raju Veeriah, Siân Harries, Jeanette Kittel, Nika Iremadze, Itai Rusinek, Gat Kreiger, Ariel Jaimovich, Jacqui Shaw, Allan Hackshaw, Nnennaya Kanu, Elena Helman, Mariam Jamal-Hanjani, Charles Swanton. Error-corrected plasma whole-genome sequencing for personalised and tumor-agnostic minimal residual disease detection in NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(8_Suppl):Abstract nr LB116.

The thymus is essential for establishing T cell diversity early in life, but undergoes profound involution with age and has therefore traditionally been regarded as largely nonfunctional in adults1,2. Here we propose that preserving thymic functionality is integral to adult health and longevity. We developed a deep learning framework to quantify thymic health from routine radiographic images and evaluated its association with longevity and risk of major age-associated diseases in two large prospective cohorts of asymptomatic adults: the National Lung Screening Trial (n = 25,031) and the Framingham Heart Study (n = 2,581). In both cohorts, thymic health varied markedly across the population. In the National Lung Screening Trial, higher thymic health was consistently associated with lower all-cause mortality, reduced lung cancer incidence and lower cardiovascular mortality over 12 years of follow-up after adjustment for age, sex, smoking and comorbidities. In the independent Framingham Heart Study cohort, higher thymic health was significantly associated with reduced cardiovascular mortality, independent of age, sex and smoking. Thymic health was further linked to systemic inflammation and metabolic dysregulation, and associated with modifiable lifestyle factors including smoking, obesity and physical activity. Together, these findings reposition the thymus as a central regulator of immune-mediated ageing and disease susceptibility in adulthood, highlighting its potential as a target for preventive and regenerative strategies to promote healthy ageing and longevity.

Lung cancer in never smokers (LCINS) is a growing global health challenge. Unlike smoking-related lung cancer, LCINS is characterized by distinct epidemiological patterns and unique molecular pathogenesis and, consequently, requires different clinical management approaches. Unfortunately, for patients with lung cancer who have never smoked, symptoms are nonspecific and often dismissed due to these patients not fitting a high-risk profile (e.g., smoker), underscoring the need for improved detection and interception. Emerging risk factors, including germline variants, clonal hematopoiesis, and environmental exposures, offer new avenues for risk stratification and preventive strategies. While low-dose computed tomography screening shows promise in high-risk subgroups, challenges remain in optimizing cost-effectiveness. Novel prevention approaches, from interleukin (IL)-1β inhibition to cancer vaccines, are under investigation. This opinion article discusses why LCINS demands unique clinical and research paradigms to address its biological complexity.

Table S1 shows the number of possible routes for different copy numbers states.

Although immunotherapy has revolutionized cancer treatment, many patients still experience limited benefit, highlighting the urgent need for improved biomarkers1. Although immunotherapy is founded on unleashing T cells2, most existing biomarkers remain tumour-centric and mainly overlook host immune competence. The thymus is a key immune organ that is crucial for T cell maturation, and we hypothesized that thymic functionality is associated with immunotherapy outcomes3. Here we show that thymic health, a radiographic measure of thymic functionality, is strongly associated with immunotherapy outcomes across several cancer types. Using a deep-learning framework applied to routine computed tomography images, we quantified thymic health in a pan-cancer cohort of 3,476 patients receiving immune checkpoint inhibitors. In patients with non-small cell lung cancer, higher thymic health was associated with reduced risks of progression and all-cause mortality. These associations remained significant across clinically relevant levels of programmed death ligand 1 (PD-L1) and tumour mutation burden. In the prospective TRACERx lung cancer study, thymic health was positively associated with T cell receptor diversity and T cell receptor excision circles, and correlated with immune-system signalling pathways, supporting radiographic thymic health as a proxy for thymic activity and adaptive immune competence. Analysis across patients with melanoma, breast cancer or renal cancer demonstrated pan-cancer relevance. Together, these findings identify thymic health as a previously unrecognized, tumour-agnostic determinant of immunotherapy efficacy, with potential implications for patient stratification, treatment timing and the development of immune-rejuvenating strategies in precision immuno-oncology.

Lung adenocarcinoma arising in individuals who have never smoked is understudied, represents a substantial global health burden, and is genomically distinct from smoking-associated disease. Zhao and colleagues have identified transcriptomic subtypes with prognostic value, including in stage I disease, supporting phenotypic state as an important determinant of outcome for lung adenocarcinoma in individuals who have never smoked. See related article by Zhao et al., p. 460.

Over several decades, therapeutic advances have transformed oncology, yet for many tumour types, survival improvements have been incremental, with substantial treatment‐related morbidity. A decisive pivot in oncology, from treating established malignancy to intercepting and preventing carcinogenesis, could deliver far greater population impact. Delivering this shift requires further mechanistic understanding of tumour initiation, validated biomarkers of premalignant progression and redesigned prevention trials in at‐risk populations. Regulatory and commercial frameworks must evolve to enable scalable molecular prevention. Such trials must deliver tolerable side effect profiles and rely on biologically validated surrogate endpoints rather than traditional survival outcomes. Cancer interception should be established as a core pillar of oncological management, alongside early detection and the therapeutic management of established disease, together creating an opportunity to reduce global disease burden at a scale that decades of therapeutic progress in advanced cancer have yet to achieve.

Despite there being a plethora of multicancer early detection tests, the National Health Service (NHS)-Galleri (ISRCTN91431511) is the only randomized controlled trial (RCT) of a multicancer liquid biopsy in a screening setting thus far. The NHS-Galleri trial has generated much debate, and it has been criticized in the medical press. Some of these criticisms stem from differing opinions over the choice of primary endpoint, others from poor reporting in statements to journalists from those not directly involved in the trial. Some of the debate is positive and relates to the speed of enrollment and the equity in participation, which have shown what is possible in large population-based RCTs. Here we explain our reasoning for undertaking the trial and designing it the way we did. We focus on the reason to consider multicancer screening and why we felt that the results from nonrandomized clinical studies of GRAIL's Galleri test justified a large RCT. We also consider the slow progress in adopting effective cancer screening historically and in reducing cancer mortality through early detection. There is a need to plan now for future research and implementation depending on the results of the trial. NHS-Galleri is the first double-blind cancer screening RCT. It also, unusually, uses late-stage cancer incidence (rather than cancer mortality) as its primary outcome.

Abstract Epigenetic remodeling is a hallmark of tumor evolution, yet the timing and clonality of promoter methylation events remain poorly defined. We investigated the spatial architecture of promoter DNA methylation in multiregion lung adenocarcinoma (LUAD) to identify clonal epigenetic alterations and evaluate their prognostic and translational relevance across cancers. Reduced representation bisulfite sequencing (RRBS) was performed on 151 tumor regions from 32 TRACERx LUAD patients with matched normal tissue. Differentially methylated regions (DMRs) were quantified for intratumor (ITH) and intertumor (ITeH) heterogeneity. Clonality was evaluated through three complementary metrics of methylation ubiquity, followed by univariate and LASSO Cox modeling. The resulting 30DMR panel, termed PROMISE, was derived through clustering concordance with TCGA LUAD and independently validated in CPTAC 3. PROMISE was subsequently tested for pancancer specificity across 18 tumor types from several publicly available sources.We identified 21,358 promoter DMRs showing a continuum of ITH and ITeH patterns. Promoters with low ITH but high ITeH, ubiquitously hypermethylated within tumors yet variable across patients, represented early clonal events significantly associated with poor survival. LASSO Cox selection yielded a 30-DMR signature encompassing genes involved in immune regulation, epithelial polarity, and TGFβ signaling. PROMISE robustly stratified patients into high and low risk groups in both TCGA LUAD and CPTAC 3 cohorts (logrank P < 0.01) and remained independent of clinicopathologic variables. Cross-cancer analyses revealed strong prognostic associations in kidney, thyroid, liver, and colorectal cancers, but minimal signal in squamous, stromal rich, or hematologic malignancies.PROMISE captures a panepithelial program of early, clonal promoter hypermethylation recurrent across multiple carcinomas and predictive of outcome in selected epithelial tumors. These findings highlight clonal methylation remodeling as an early determinant of tumor evolution and nominate PROMISE as a clinically actionable biomarker for cancer risk stratification. Citation Format: Francisco Gimeno-Valiente, Constantino De La Vega, Yun-Hsin Liu, Carla Castignani, Ieva Usaite, Martín Arana Jorge, Elrick Hillary, Stephan Beck, Miljana Tanic, Jonas Demeulemeester, Peter Van Loo, Charles Swanton, Mariam Jamal-Hanjani, Nnennaya Kanu. PROMISE, a clonal promoter methylation signature capturing early epigenetic evolution and prognostic programs across epithelial cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 3197.