Biology subjects

Birkbak, N. J.

Publications and source records attributed to Birkbak, N. J..

6 recordsLinked to original sources

bioRxiv2026

Preoperative thymic output and T cell repertoire diversity are associated with recurrence after nephrectomy for localized renal cell carcinoma

Radiographic thymic health and peripheral T-cell repertoire features have been linked to outcomes in renal cell carcinoma (RCC), but their prognostic value after curative-intent surgery is unclear. We quantified preoperative blood signal-joint T-cell receptor excision circles (sjTRECs), a marker of thymic output, in 218 patients with localized RCC undergoing nephrectomy and characterized T-cell receptor {beta} (TCR{beta}) repertoires in 201 patients. We assessed overall survival (OS) and recurrence-free survival (RFS) using Kaplan-Meier and Cox models adjusted for age, sex, and Leibovich risk group. High sjTREC levels were associated with longer RFS after adjustment for age, sex, and Leibovich risk group (hazard ratio [HR] 0.50; 95% confidence interval [CI], 0.29-0.87; p=0.015), with a concordant OS estimate (HR 0.62; 95% CI, 0.38-1.02; p=0.058). sjTREC provided additional prognostic information beyond Leibovich risk stratification for recurrence overall and among intermediate/high-risk patients (likelihood-ratio test, p=0.024 and p=0.034, respectively). Higher TCR{beta} diversity was associated with longer RFS overall (HR 0.76; 95% CI, 0.60-0.96; p=0.024) and among intermediate/high-risk patients with longer RFS (HR 0.71; 95% CI, 0.55-0.92; p=0.009) and OS (HR 0.80; 95% CI, 0.65-0.98; p=0.031). Preoperative sjTREC provided prognostic information beyond clinicopathological risk, with higher TCR{beta} diversity associated with favorable outcomes.

cancer biology↗

bioRxiv2024

Comprehensive characterization of the T cell receptor repertoire in bladder cancer

T cells are one of the primary effector cells in the endogenous defense against cancer, yet the clinical impact of their quantity, diversity, and dynamics remains underexplored. Here we investigated the clinical relevance of the T cell receptor (TCR) repertoire in patients with bladder cancer. In advanced-stage bladder cancer, low pre-treatment peripheral TCR diversity was associated with worse overall survival (p=0.024), particularly when it coincided with a low fraction of circulating T cells (p=0.00049). The low-diversity TCR repertoires were dominated by expanded clones that persisted throughout treatment and disproportionately targeted latent viral infections. Longitudinal analysis revealed a reduction in TCR diversity after treatment indicating an adverse effect on the immune system. In early-stage bladder cancer, we showed that immunotherapy had a stimulatory effect on TCR diversity in patients with good outcomes. Single-cell sequencing identified most expanded clones as cytotoxic T cells, while non-expanded clones were predominantly naive T cells. Overall, our findings suggest that TCR diversity is a promising new biomarker that may offer new avenues for tailored oncological treatment to enhance clinical outcomes for bladder cancer patients.

cancer biology↗

bioRxiv2023

Endogenous viral elements constitute a complementary source of antigens for personalized cancer immunotherapy

Personalized cancer vaccines (PCVs) largely leverage neoantigens arising from somatic mutations limiting their application to patients with relatively high tumor mutational burden (TMB). This underscores the need for alternative antigens to design PCVs for low TMB cancers. To this end, we substantiate endogenous retroviral elements (EVEs) as tumor antigens through large-scale genomic analyses of healthy tissues and solid cancers. These analyses revealed that the breadth of EVE expression in tumors stratify checkpoint inhibitor treated melanoma patients into groups with differential overall and progression-free survival. To enable the design of PCVs containing EVE-derived epitopes with therapeutic potential, we developed a computational pipeline, ObsERV. We show that EVE-derived peptides are presented as epitopes on tumors and can be predicted by ObsERV. Preclinical testing of ObsERV demonstrates induction of sustained poly-functional CD4+ and CD8+ T-cell responses as well as long-term tumor protection. As such, EVEs may facilitate and improve PCVs especially for low-TMB patients.

cancer biology↗

bioRxiv2022

The ratio of adaptive to innate immune cells differs between genders and associates with improved prognosis and response to immunotherapy

Immunotherapy has revolutionised cancer treatment. However, not all cancer patients benefit, and current stratification strategies based primarily on PD1 status and mutation burden is far from perfect. We hypothesised that high activation of an innate response relative to the adaptive response may prevent proper tumour neoantigen identification and decrease the specific anticancer response, both in the presence and absence of immunotherapy. To investigate this, we obtained transcriptomic data from three large publicly available cancer datasets, the Cancer Genome Atlas (TCGA), the Hartwig Medical Foundation (HMF), and a recently published cohort of metastatic bladder cancer patients treated with immunotherapy. To analyse immune infiltration into bulk tumours, we developed an RNAseq-based model based on previously published definitions to estimate the overall level of infiltrating innate and adaptive immune cells from bulk tumour RNAseq data. From these, the adaptive-to-innate immune ratio (A/I ratio) was defined. A meta-analysis of 32 cancer types from TCGA overall showed improved overall survival in patients with an A/I ratio above median (Hazard ratio (HR) females 0.73, HR males 0.86, P < 0.05). Of particular interest, we found that the association was different for males and females for eight cancer types, demonstrating a gender bias in the relative balance of the infiltration of innate and adaptive immune cells. For patients with metastatic disease, we found that responders to immunotherapy had a significantly higher A/I ratio than non-responders in HMF (P = 0.036) and a significantly higher ratio in complete responders in a separate metastatic bladder cancer dataset (P = 0.022). Overall, the adaptive-to-innate immune ratio seems to define separate states of immune activation, likely linked to fundamental immunological reactions to cancer. This ratio was associated with improved prognosis and improved response to immunotherapy, demonstrating potential relevance to patient stratification. Furthermore, by demonstrating a significant difference between males and females that associates with response, we highlight an important gender bias which likely has direct clinical relevance.

bioinformatics↗

bioRxiv2019

Whole Genome Doubling mitigates Muller’s Ratchet in Cancer Evolution

Whole genome doubling (WGD) is a prevalent macro-evolutionary event in cancer, involving a doubling of the entire chromosome complement. However, despite its prevalence and clinical prognostic relevance, the evolutionary selection pressures for WGD have not been investigated. Here, we explored whether WGD may act to mitigate the irreversible, inexorable ratchet-like, accumulation of deleterious mutations in essential genes. Utilizing 1050 tumor regions from 816 non-small cell lung cancers (NSCLC), we temporally dissect mutations to determine their temporal acquisition in relation to WGD. We find evidence for strong negative selection against homozygous loss of essential cancer genes prior to WGD. However, mutations in essential genes occurring after duplication were not subject to significant negative selection, consistent with WGD providing a buffering effect, decreasing the likelihood of homozygous loss. Finally, we demonstrate that loss of heterozygosity and temporal dissection of mutations can be exploited to identify signals of positive selection in lung, breast, colorectal cancer and other cancer types, enabling the elucidation of novel tumour suppressor genes and a deeper characterization of known cancer genes.

genomics↗

bioRxiv2017

Evolution and clinical impact of genetic epistasis within EGFR-mutant lung cancers

Introductory paragraph Introductory paragraph Main text Methods Author Contributions Author Information References The current understanding of tumorigenesis is largely centered on a monogenic driver oncogene model. This paradigm is incompatible with the prevailing clinical experience in most solid malignancies: monotherapy with a drug directed against an individual oncogenic driver typically results in incomplete clinical responses and eventual tumor progression1-7. By profiling the somatic genetic alterations present in over 2,000 cases of lung cancer, the leading cause of cancer mortality worldwide8,9, we show that combinations of functional genetic alterations, i.e. genetic collectives dominate the landscape of ...

cancer biology↗