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  • Complex rearrangements fuel ER+ and HER2+ breast tumours. Nature Houlahan, K. E., Mangiante, L., Sotomayor-Vivas, C., Adimoelja, A., Park, S., Khan, A., Pribus, S. J., Ma, Z., Caswell-Jin, J. L., Curtis, C. 2025

    Abstract

    Breast cancer is a highly heterogeneous disease whose prognosis and treatment as defined by the expression of three receptors-oestrogen receptor (ER), progesterone receptor and human epidermal growth factor receptor 2 (HER2; encoded by ERBB2)-is insufficient to capture the full spectrum of clinical outcomes and therapeutic vulnerabilities. Previously, we demonstrated that transcriptional and genomic profiles define eleven integrative subtypes with distinct clinical outcomes, including four ER+ subtypes with increased risk of relapse decades after diagnosis1,2. Here, to determine whether these subtypes reflect distinct evolutionary histories, interactions with the immune system and pathway dependencies, we established a meta-cohort of 1,828 breast tumours spanning pre-invasive, primary invasive and metastatic disease with whole-genome and transcriptome sequencing. We demonstrate that breast tumours fall along a continuum constrained by three genomic archetypes. The ER+ high-risk integrative subgroup is characterized by complex focal amplifications, similar to HER2+ tumours, including cyclic extrachromosomal DNA amplifications induced by ER through R-loop formation and APOBEC3B-editing, which arise in pre-invasive lesions. By contrast, triple-negative tumours exhibit genome-wide instability and tandem duplications and are enriched for homologous repair deficiency-like signatures, whereas ER+ typical-risk tumours are largely genomically stable. These genomic archetypes, which replicate in an independent cohort of 2,659 primary tumours, are established early during tumorigenesis, sculpt the tumour microenvironment and are conserved in metastatic disease. These complex structural alterations contribute to replication stress and immune evasion, and persist throughout tumour evolution, unveiling potential vulnerabilities.

    View details for DOI 10.1038/s41586-024-08377-x

    View details for PubMedID 39779850

    View details for PubMedCentralID 6172658

  • Increasing equity in science requires better ethics training: A course by trainees, for trainees. Cell genomics Patel, R. A., Ungar, R. A., Pyke, A. L., Adimoelja, A., Chakraborty, M., Cotter, D. J., Freund, M., Goddard, P., Gomez-Stafford, J., Greenwald, E., Higgs, E., Hunter, N., MacKenzie, T. M., Narain, A., Gjorgjieva, T., Martschenko, D. O. 2024: 100554

    Abstract

    Despite the profound impacts of scientific research, few scientists have received the necessary training to productively discuss the ethical and societal implications of their work. To address this critical gap, we-a group of predominantly human genetics trainees-developed a course on genetics, ethics, and society. We intend for this course to serve as a template for other institutions and scientific disciplines. Our curriculum positions human genetics within its historical and societal context and encourages students to evaluate how societal norms and structures impact the conduct of scientific research. We demonstrate the utility of this course via surveys of enrolled students and provide resources and strategies for others hoping to teach a similar course. We conclude by arguing that if we are to work toward rectifying the inequities and injustices produced by our field, we must first learn to view our own research as impacting and being impacted by society.

    View details for DOI 10.1016/j.xgen.2024.100554

    View details for PubMedID 38697124