Citations

ABSTRACT Germline variation shapes cancer risk, yet its influence on the evolutionary dynamics of established tumors remains poorly understood. In multiple myeloma, subclonal diversification drives disease progression and treatment failure, but the heritable factors that modulate this process are unknown. Here, we show that germline variation is associated with tumor evolutionary features, implicating inherited regulation in subclonal expansion. Integrating germline variation with tumor evolutionary parameters identifies variants associated with evolutionary features, with signals enriched in regulatory regions, consistent with a transcriptional basis. We further identify TBKBP1 as a key locus linking germline variation to tumor evolution and clinical outcome. Germline variation at this locus is associated with TBKBP1 expression and subclonal expansion, and TBKBP1 expression correlates with adverse prognosis, consistent across independent cohorts. Functional analyses demonstrate that TBKBP1 promotes proliferation and activates MYC, mTORC1 and non-canonical NF-κB signaling pathway. Together, these findings establish germline regulatory variation as a determinant of tumor evolutionary dynamics and identify TBKBP1 as a mediator linking inherited variation to subclonal expansion and disease progression in multiple myeloma.

8045 Background: Surgical resection is the primary therapy for stage I-II NSCLC but not performed in a subset of patients due to comorbidities or self-election, who instead undergo radiation with or without systemic therapy (RT±ST). Little is known about the demographic, tumoral, therapeutic, and quality-of-life (QOL) characteristics of this non-surgical group. Understanding their differences from the surgical group is essential for developing precision treatment strategies and tailored survivorship guidelines. Methods: In a prospectively enrolled (1997-2016) and followed (through 2025) cohort of 20,951 primary lung cancer patients, 6,486 (31%) had stage I-II NSCLC, including 5,359 (83%) treated surgically (Surgical) and 1,113 (17%) otherwise (Non-surgical). Preexisting diseases were grouped into cancer, lung, and other comorbidities. QOL data were available for 40% of all patients. Descriptive analysis of demographics, tumor features, treatment patterns, and QOL metrics, as well as survival analysis (median years and overall survival [OS] rates) were conducted. QOL measures, on overall and 15 symptom and functional domains, were scored 0 (worst) to 10 (best), with 1-unit difference considered clinically and statistically meaningful. Results: At time of diagnosis, compared to the Surgical, the Non-surgical patients were older (median 73 v 68 years), more likely to have smoked cigarettes (91% v 83%), squamous cell and unspecified NSCLC (53% v 28%), stage IIB (19% v 12%), and preexisting lung comorbidities (71% v 58%). Non-surgical patients more frequently received RT±ST than the Surgical (70% v 21%) and had shorter median survival (2.5 v 7.8) years. Within the Non-surgical, 28% had no cancer treatment (No-Tx), 44% RT-only, 7% ST-only, and 19% both (RT+ST); their respective median diagnosis ages were 74, 76, 68, 70 years; median survival were 1.7, 2.7, 2.2, 3.2 years; 5-year OS (95%CI) at 25% (21-31), 25% (21-29), 26% (17-38), 30% (25-37); and 10-year OS at 9% (7-14), 7% (5-10), 10% (5-21), 9% (6-14), respectively. RT-only group had highest rates of comorbidities (37-84%) and the No-Tx the lowest (31-66%). Although the overall QOL scored the same for all groups, RT-only patients reported the worst scores on multiple symptoms burden, and the No-Tx reported the least pain and lung cancer symptoms but the worst on mental well-being and social activities. Conclusions: Non-surgically managed stage I-II NSCLC cases present clinically distinct patients with the shortest median survival in No-Tx group and highest 5-year survival in RT+ST. RT-only patients were oldest, had the most comorbidities, and reported the worst symptom burdens. These differences highlight the need for more in-depth analyses and studies (considering age, histology, comorbidity, QOL, etc.) to support tailored therapeutic strategies and survivorship care for patients who decline or are not suitable for surgery.

Abstract Expression quantitative trait locus (eQTL) mapping is used to identify the functional link between a genomic variant and a gene’s expression. A significant eQTL association does not mean a causal relationship or mechanism, and further investigation is needed to understand how a single-nucleotide polymorphism (SNP) impacts gene expression. One of the most plausible explanations for eQTL is that a genomic variant affects transcription factor (TF) binding and thus impacts its regulation on target genes (TGs). However, the current eQTL model does not provide information on the TF and how its regulation is mediated by the SNP’s genotypes. Here, we propose a new method called differential co-expression QTL (ceQTL) among different alleles using Chow statistics to specifically detect eQTLs that are bound by a particular TF. We start with building a trio of TF, its TG, and related SNP, and then test the significant coefficient difference among different genotypes of the SNP. We applied this ceQTL model to simulated data and the lung tissue datasets from the genotype-tissue expression project. The simulated data results showed that the model was robust to detect true ceQTLs at variable sample sizes and different minor allele frequencies as measured by area under the curve. Our tool also performed a TF binding affinity analysis to add another layer of evidence for functional interpretation. In summary, ceQTL analysis provides a more interpretable and biological insight into the mechanism of eQTL and transcriptomic regulation, which would help us better understand how genomic variants affect phenotypes and diseases.

Abstract Motivation Intratumor heterogeneity arises from ongoing somatic evolution and complicates cancer diagnosis, prognosis, and treatment. Reconstructing evolutionary dynamics typically requires spatiotemporal samples, which are often unavailable in clinical settings. Computational approaches that can infer tumor evolutionary history from single-timepoint bulk sequencing data remain limited. Results We present estimating evolutionary events through single-timepoint sequencing (TEATIME), a novel computational framework that models tumors as mixtures of two competing cell populations: an ancestral clone with baseline fitness and a derived subclone with elevated fitness. Using cross-sectional bulk sequencing data, TEATIME estimates mutation rates, timing of subclone emergence, relative fitness, and number of generations of growth. To quantify intratumor fitness asymmetries, we introduce a novel metric—fitness diversity—which captures the imbalance between competing cell populations and serves as a measure of functional intratumor heterogeneity. Applying TEATIME to 33 tumor types from The Cancer Genome Atlas, we revealed divergent as well as convergent evolutionary patterns. Notably, we found that immune-hot microenvironments constraint subclonal expansion and limit fitness diversity. Moreover, we detected temporal dependencies in mutation acquisition, where early driver mutations in ancestral clones epistatically shape the fitness landscape, predisposing specific subclones to selective advantages. These findings underscore the importance of intratumor competition and tumor-microenvironment interactions in shaping evolutionary trajectories, driving intratumor heterogeneity. Lastly, we demonstrate that TEATIME-derived evolutionary parameters and fitness diversity offer novel prognostic insights across multiple cancer types. Availability and implementation R implementation of TEATIME is available on GitHub (https://github.com/liliulab/TEATIME) and Zenodo (https://zenodo.org/records/17422174).

Abstract Objective To investigate the ability of artificial intelligence‐enabled electrocardiogram (AI‐ECG) atrial fibrillation (AF) prediction model output and delta age, defined as AI‐estimated age minus chronological age, to predict adverse vascular outcomes in patients with migraine. Background Migraine, especially migraine with aura, is associated with an increased risk of cardiovascular events. Using normal sinus rhythm ECG, our institution has developed AI‐ECG models that predict the probability of AF and estimate patients' age, and from that, delta age (estimated age minus actual age) has been shown to reflect cardiovascular health and physiologic aging. Methods We conducted a retrospective cohort study that included adult patients with migraine who had at least one digital, standard 12‐lead ECG from 2000 to 2020 at any Mayo Clinic site. The first normal sinus rhythm ECG was defined as the index ECG, and those with adverse vascular events or AF prior to, or within 3 days after, index ECG were excluded. AI‐ECG AF prediction model output and delta age were obtained from the index ECG. The primary outcome was a composite endpoint of adverse vascular events that included acute myocardial infarction, acute ischemic stroke, venous thromboembolism, and death. New‐onset AF was also recorded as a secondary outcome. Results A total of 29,928 patients were included. The mean age was 44.3 ± 14.5 years, and the median follow‐up time was 54 months. During the study period, 4662 (15.6%) patients had adverse vascular events, and 1384 (4.6%) patients developed new‐onset AF. A higher AF prediction model output was associated with a higher risk of adverse vascular outcomes (adjusted hazard ratio [aHR]:1.15 [95% confidence interval: 1.12 to 1.18] for every 10% increase in prediction model output), as was a larger delta age (aHR:1.16 [1.12 to 1.21] for every 10‐year increase in delta age). Moreover, AI‐ECG AF prediction model outputs of ≥1% (aHR: 1.45 [1.36 to 1.54]) and delta age ≥−1 years (aHR: 1.09 [1.02 to 1.16]) were found to be the optimal cutoffs to dichotomize patients into high‐risk and low‐risk groups for adverse vascular events. Higher AI‐ECG AF prediction model output at baseline also predicted a higher likelihood of having new‐onset AF during the study period (aHR: 1.31 [1.26 to 1.37]), and the development of new‐onset AF was associated with a higher risk of adverse vascular events (aHR: 2.43 [2.17 to 2.73]). Conclusions For patients with migraine, a higher AI‐ECG AF prediction model output and delta age are predictive of adverse vascular outcomes. A higher AF prediction model output is also predictive of future AF development. Furthermore, we identified the cutoffs for both AI‐ECG models that can distinguish patients between high‐ and low‐risk groups. Our results showed that AI‐ECG models could inform clinical practice and identify patients with migraine at risk for future adverse vascular events.