Copy number footprints of platinum-based anticancer therapies

Structural variant and nucleosome occupancy dynamics postchemotherapy in a HER2+ breast cancer organoid model

The most common chemotherapeutics induce DNA damage to eradicate cancer cells, yet defective DNA repair can propagate mutations, instigating therapy resistance and secondary malignancies. Structural variants (SVs), arising from copy-number-imbalanced and -balanced DNA rearrangements, are a major driver of tumor evolution, yet understudied posttherapy. Here, we adapted single-cell template-strand sequencing (Strand-seq) to a HER2+ breast cancer model to investigate the formation of doxorubicin-induced de novo SVs. We coupled this approach with nucleosome occupancy (NO) measurements obtained from the same single cell to enable simultaneous SV detection and cell-type classification. Using organoids from TetO-CMYC/TetO-Neu/MMTV-rtTA mice modeling HER2+ breast cancer, we generated 459 Strand-seq libraries spanning various tumorigenesis stages, identifying a 7.4-fold increase in large chromosomal alterations post-doxorubicin. Complex DNA rearrangements, deletions, and duplications were prevalent across basal, luminal progenitor (LP), and mature luminal (ML) cells, indicating uniform susceptibility of these cell types to SV formation. Doxorubicin further elevated sister chromatid exchanges (SCEs), indicative of genomic stress persisting posttreatment. Altered nucleosome occupancy levels on distinct cancer-related genes further underscore the broad genomic impact of doxorubicin. The organoid-based system for single-cell multiomics established in this study paves the way for unraveling the most important therapy-associated SV mutational signatures, enabling systematic studies of the effect of therapy on cancer evolution.

Impact of chemoradiotherapy for first primary lung cancer on the prognosis and re-chemoradiotherapy sensitivity of second primary lung cancer

Background

Despite undergoing surgery and chemoradiotherapy, patients with first primary lung cancer (FPLC) remain at risk for second primary lung cancer (SPLC), which is associated with a poor prognosis. The effects of FPLC chemoradiotherapy on SPLC prognosis and its sensitivity to re-chemoradiotherapy have not been adequately investigated.

Methods

This cohort study analyzed data from 23,827 patients who underwent FPLC surgery during 1973-2021, drawn from the Surveillance, Epidemiology, and End Results database. Among these, 5,302 FPLC patients developed SPLC within 5 years of their initial diagnosis. We employed the Fine-Gray competitive risk model, Cox proportional hazards model, and restricted mean survival time analysis to assess the effects of FPLC radiotherapy and chemotherapy on SPLC risk and survival differences.

Results

The competitive risk model indicated that FPLC radiotherapy and chemotherapy did not significantly change the risk of developing SPLC. However, the Cox proportional hazards model revealed that FPLC radiotherapy was associated with decreased overall survival (OS; HR=1.251, P<0.001) and cancer-specific survival (CSS; HR=1.228, P=0.001) in patients with SPLC. Conversely, FPLC chemotherapy was linked to improved OS (HR=0.881, P=0.012) in this population. Patients with SPLC who received combined chemoradiotherapy for FPLC exhibited significantly reduced survival times (OS: HR=1.157, P=0.030; CSS: HR=1.198, P=0.018), a finding confirmed across multiple models. For SPLC patients with prior FPLC chemoradiotherapy, subsequent SPLC radiotherapy significantly improved prognosis. Notably, this benefit is even more pronounced in patients who have not received prior chemoradiotherapy. While SPLC chemotherapy enhanced OS for patients who did not receive FPLC chemotherapy, it was associated with reduced CSS for those who had.

Conclusions

Overall, FPLC chemoradiotherapy influences SPLC prognosis and influences sensitivity to treatment. Tailoring SPLC management to FPLC treatment regimens may improve survival outcomes.

Evaluating offspring Genomic and Epigenomic alterations after prenatal exposure to Cancer treatment In Pregnancy (GE-CIP): a multicentric observational study

INTRODUCTION

Around 1 in 1000-2000 pregnancies are affected by a cancer diagnosis. Previous studies have shown that chemotherapy during pregnancy has reassuring cognitive and cardiac neonatal outcomes, and hence has been proposed as standard of care. However, although these children perform within normal ranges for their age, subtle differences have been identified. Given that chemotherapeutic compounds can cross the placenta, the possibility that prenatal chemotherapy exposure mutates the offspring's genome and/or epigenome, with potential deleterious effects later in life, urges to be investigated.

METHODS AND ANALYSES

This multicentric observational study aims to collect cord blood, meconium and neonatal buccal cells at birth, as well as peripheral blood, buccal cells and urine from infants when 6, 18 and/or 36 months of age. Using bulk and single-cell approaches, we will compare samples from chemotherapy-treated pregnant patients with cancer, pregnant patients with cancer not treated with chemotherapy and healthy pregnant women. Potential chemotherapy-related newborn genomic and/or epigenomic alterations, such as single nucleotide variants, copy number variants and DNA-methylation alterations, will be identified in mononuclear and epithelial cells, isolated from blood, buccal swabs and urine. DNA from maternal peripheral blood and paternal buccal cells will be used to determine de novo somatic mutations in the neonatal blood and epithelial cells. Additionally, the accumulated exposure of the fetus, and biological effective dose of alkylating agents, will be assessed in meconium and cord blood via mass spectrometry approaches.

ETHICS AND DISSEMINATION

The Ethics Committee Research of UZ/KU Leuven (EC Research) and the Medical Ethical Review Committee of University Medical Center Amsterdam have approved the study. Results of this study will be disseminated via presentations at (inter)national conferences, through peer-reviewed, open-access publications, via social media platforms aimed to inform patients and healthcare workers, and through the website of the International Network on Cancer, Infertility and Pregnancy (www.cancerinpregnancy.org).