The researchers applied single-cell RNA sequencing technology to dissect thousands of individual mammary epithelial cells from aged female mice that had either experienced an early first pregnancy or remained nulliparous (never pregnant). This approach allowed unprecedented resolution in characterizing cellular heterogeneity and gene expression dynamics within the aging mammary gland, providing critical insights into lineage commitment and cellular identity. Their analysis exposed a previously unrecognized subset of “hybrid” epithelial cells in aged, nulliparous mice. These cells defy normal classification by simultaneously expressing markers of both luminal and basal mammary lineages, suggesting a breakdown in cellular differentiation fidelity—a phenomenon now linked with increased tumor risk.

A central molecular player surfaced from this study: Interleukin-33 (IL-33), an inflammatory cytokine markedly elevated in the hybrid cell population. IL-33 not only serves as a biomarker for these confused cells but also actively drives features reminiscent of early tumorigenesis. When young mammary epithelial cells were experimentally exposed to IL-33 in vitro, they exhibited enhanced proliferative capacity and formed organoids more readily, especially in the absence of functional Trp53, a crucial tumor suppressor gene. This finding implicates IL-33 as a potent inducer of cellular plasticity and proliferation, likely fostering a microenvironment conducive to malignant transformation.

Intriguingly, early pregnancy appears to act as a “cellular reset button,” preventing the emergence and accumulation of these IL-33–positive hybrid populations during mammary aging. The process seems to enforce a stringent lineage integrity, compelling cells to commit to their specialized roles and maintaining tissue homeostasis. This mechanism provides a biological rationale for the long-observed protective effect of early childbirth, which may only manifest decades later despite occurring much earlier in life. By stabilizing cell identity and suppressing pro-tumorigenic signals, pregnancy effectively rewires the mammary gland’s aging process.

The implications of these findings are profound when contextualizing breast cancer epidemiology. Most breast cancer cases are diagnosed post-menopause, a stage mimicked here by studying aged mice beyond reproductive years. Yet the protective influence of a pregnancy decades earlier reprograms the aging breast at the molecular and cellular levels, highlighting the significance of early reproductive history in modulating cancer risk. This delayed effect reflects the slow accrual of cellular abnormalities that pregnancy helps to mitigate, an insight that fundamentally advances our understanding of breast tissue aging and oncogenesis.

Further analysis revealed that pregnancy restored the balance between basal and luminal mammary epithelial cells, which otherwise becomes skewed with aging. Typically, basal cells expand disproportionately in aged nulliparous mice, a shift reversed by parity. Functional assays demonstrated that both basal and luminal cells from aged parous animals formed fewer organoids, indicative of reduced proliferative potential and possibly a lowered risk of malignant transformation. Moreover, luminal cells in parous mice retained molecular hallmarks of post-pregnancy involution—a state known to stimulate immune surveillance—suggesting an additional cancer-protective mechanism actively engaging the immune system.

The discovery of IL-33’s role in fostering hybrid epithelial cells elucidates a key link between inflammation, cellular plasticity, and oncogenesis within the breast. Inflammatory signaling has long been implicated in tumor biology, but this study places IL-33 at a central crossroads, mediating age-dependent cellular confusion that might initiate carcinogenesis. By experimentally exposing cells to IL-33 and suppressing Trp53, the researchers recreated conditions facilitating early tumor development, underscoring how aging and inflammatory pathways converge to drive malignant progression.

While this study was performed in mice, the authors emphasize the conserved architecture of mammary glands and analogous epidemiological patterns of breast cancer risk in humans, suggesting translational relevance. The elucidation of hybrid cell populations and their regulation by pregnancy offers novel targets for preventative strategies, potentially transforming how at-risk women are monitored or treated. Interventions that mimic pregnancy’s stabilizing influence on mammary cells or therapeutically modulate IL-33 signaling could emerge as innovative means to forestall breast cancer.

Although definitive proof connecting hybrid cells to cancer formation in humans is pending, the identification of this cell population as a biomarker and functional contributor to tumorigenic processes marks a significant advance. The researchers plan to delve deeper into the biology and regulation of these cells, aiming to unravel how lineage instability evolves and whether it directly precipitates malignancy. Their future work may also explore how immune mechanisms interact with cellular identity programs during mammary aging.

Ultimately, this study reframes the narrative around pregnancy and breast cancer by highlighting pregnancy not merely as a reproductive milestone but as a powerful biological modulator that permanently affects cellular aging trajectories. The protective legacy of early pregnancy reflects a profound reprogramming of mammary gland biology, emphasizing the interplay between developmental history and cancer susceptibility. These insights open avenues for novel diagnostic and therapeutic approaches focused on maintaining cellular fidelity and quelling inflammatory drivers in the aging breast.

This research was led by Shaheen Sikandar, an assistant professor at UC Santa Cruz’s Department of Molecular, Cell, and Developmental Biology. Co-authors included Paloma Medina, Veronica Haro Acosta, Sara Kaushik, and Matijs Dijkgraaf, all of whom contributed to the interdisciplinary effort involving genomics, stem cell biology, and molecular oncology. Funded by the Hellman Foundation and NIH’s National Cancer Institute fellowship program, this work propels the field toward a nuanced understanding of cancer risk shaped by lifelong biological processes.

For decades, breast cancer has posed a complex puzzle, where age and reproductive history intersect to influence disease onset. The elucidation of IL-33+ hybrid epithelial cells and their suppression through early pregnancy provides a transformative framework to conceptualize breast tissue aging and cancer prevention. As the scientific community builds upon these findings, hope emerges for tailored interventions that replicate pregnancy’s protective effects, dramatically altering breast cancer trajectories and improving outcomes worldwide.

Subject of Research: Animals

Article Title: Divergent aging of nulliparous and parous mammary glands reveals IL33+ hybrid epithelial cells

News Publication Date: 21-Jan-2026

Web References:
DOI link

Image Credits: Sikandar Lab / UC Santa Cruz

Keywords: breast cancer, aging, mammary gland, pregnancy, IL-33, hybrid epithelial cells, cell differentiation, inflammation, single-cell RNA sequencing, tumor suppression, Trp53, cellular plasticity

The human brain, a marvel of biological complexity, is subject to subtle yet profound changes throughout a person’s life. Recently, groundbreaking research employing state-of-the-art single-cell technologies has uncovered how the genetic and transcriptomic architecture within brain cells evolves during ageing. These discoveries shed light on the intricate interplay between somatic mutations—those acquired during life—and gene expression dynamics, providing unprecedented insights into the molecular underpinnings of brain ageing.

Leveraging combined single-nucleus RNA sequencing (snRNA-seq), single-cell whole-genome sequencing (scWGS), and spatial transcriptomics, researchers meticulously mapped both genome-wide mutations and the corresponding transcriptomes of individual brain cells. This multi-faceted approach revealed a striking trend: short, highly expressed housekeeping genes—genes essential for core cellular functions—accumulate significantly more somatic single-nucleotide variants (sSNVs) over time. Intriguingly, this rise in mutation burden correlates strongly with a decrease in the expression levels of these crucial housekeeping genes.

A closer examination offers compelling evidence supporting this novel insight. Firstly, the enriched gene ontology terms related to housekeeping functions predominated among downregulated genes, particularly in neurons, whereas neuron-specific genes maintained relatively stable expression profiles during ageing. This suggests that ageing selectively impacts fundamental cellular maintenance processes rather than cell identity programs. Secondly, the study confirmed that housekeeping genes tend to be both short and robustly expressed, aligning with known genomic properties. Notably, the highest sSNV rates appeared in the shortest, most actively transcribed housekeeping genes.

Further statistical analysis unveiled a nuanced relationship capturing how these variables intersect. A multiple linear regression model demonstrated that elevated gene expression increased the likelihood of transcriptional downregulation with age, whereas longer gene length was associated with either preservation or even upregulation of transcriptional activity during ageing. These findings are particularly illuminating given the longstanding but inconsistent observations about gene length effects in ageing across various tissues. Within neurons, it appears that the transcriptional landscape favors retention of long, identity-defining genes while allowing somatic mutagenesis to erode short housekeeping genes.

The biological mechanisms driving these patterns are multifaceted. One plausible explanation posits that somatic mutations introduce premature stop codons or disrupt splicing fidelity, triggering nonsense-mediated decay pathways that reduce transcript abundance of affected genes. Additionally, faulty or aberrant DNA repair mechanisms implicated in the formation of somatic mutations could result in local epigenetic dysregulation, further influencing gene expression changes during ageing. Another fascinating aspect is the potential differential efficacy of DNA repair machinery between gene classes; short, highly expressed housekeeping genes may bear a higher burden due to their preferential engagement in transcription-coupled DNA repair (TCR).

Recent studies have revealed that single-stranded DNA lesions, often a precursor to mutations, can persist in human cells for extended durations without active repair, raising the possibility that transcription processes themselves may convert DNA damage into fixed, double-stranded mutations. Given that neurons are post-mitotic—non-dividing—and express high levels of topoisomerases that safeguard long genes, this cellular context may amplify the accumulation of mutations selectively in short housekeeping genes rather than the long neuron-specific genes.

Beyond these molecular insights, the research offers a rich portrait of cellular composition changes across the human lifespan. In infant brains, distinct populations of immature neurons and astrocytes were detected, along with an elevated ratio of oligodendrocyte precursor cells relative to their mature counterparts, supporting ongoing postnatal brain development. These developmental insights are complemented by the genomic profiling of somatic mutations in ageing neurons, which captured an increase in sSNVs with mutational spectra reminiscent of COSMIC mutational signatures SBS5 and SBS30, both previously linked to age-related mutagenesis and DNA damage responses.

Delving deeper, two novel mutational signatures designated A1 and A2 emerged from de novo analyses. Signature A1, characterized predominantly by T>C transitions, clustered with the clock-like SBS5 signature and showed enrichment in highly expressed genes, coding regions, and genomic loci marked by open chromatin. In contrast, Signature A2, dominated by C>T transitions and enriched in C>A and T>C variants associated with oxidative DNA damage, resembled the SBS30 signature but exhibited distinct enrichment in non-coding, repressed chromatin domains with repressive epigenetic marks.

The dynamic expression profiles of DNA base excision repair proteins, particularly NTHL1 and OGG1, within neurons across ageing provide tantalizing clues linking cellular repair activity to mutational signatures. While NTHL1’s decreased activity has been connected to SBS30 in other contexts, OGG1 involvement aligns with neuronal C>A mutations. The interplay between these repair pathways and accumulating somatic mutations likely shapes both the mutational landscape and transcriptomic alterations observed during neuronal ageing.

Crucially, the study’s comprehensive single-cell approach sets a new standard for exploring how somatic mutations intertwine with gene expression heterogeneity in distinct brain cell types. As single-cell whole-genome sequencing technologies continue to mature and expand across diverse cell populations, future investigations promise to unravel more intricate connections between somatic genomic alterations and functional consequences in the ageing brain.

This pioneering work not only deepens understanding of fundamental ageing biology but also paves the way for targeted interventions. By revealing vulnerabilities in housekeeping genes stemming from mutation accumulation and transcriptional changes, it opens potential therapeutic avenues aimed at preserving cellular homeostasis and delaying neurodegeneration. Moreover, the differential resilience of neuron identity genes hints at innate protective mechanisms that could be harnessed or augmented.

Altogether, this research exemplifies an integrative multi-omic leap forward in deciphering the genomic and transcriptomic choreography unfolding across human brain lifespan. It paints a detailed molecular narrative where mutation-driven erosion of essential housekeeping genes contrasts with preservation of cell identity programs, offering a refined lens through which to view ageing’s impact on brain health.

As the intersection of genetics, epigenetics, and transcriptomics continues to be illuminated at single-cell resolution, our grasp of brain ageing mechanisms will sharpen, enabling precision medicine strategies attuned to the unique vulnerabilities and strengths of neural circuits. The implication of transcription-coupled repair and mutational signatures further links genome maintenance processes to functional ageing, suggesting new biomarkers and targets for intervention.

Ultimately, this transformative research advances the frontier of neuroscience, calling attention to the silent genomic shifts that accumulate imperceptibly but inexorably within our brain cells, shaping cognition, resilience, and healthspan. Understanding these molecular changes is vital as populations age worldwide and the burden of neurodegenerative diseases rises, highlighting the promise of genomic and transcriptomic studies in the quest for healthier brain ageing.

Subject of Research: Single-cell transcriptomic and genomic changes during human brain ageing.

Article Title: Single-cell transcriptomic and genomic changes in the ageing human brain.

Article References:
Jeffries, A.M., Yu, T., Ziegenfuss, J.S. et al. Single-cell transcriptomic and genomic changes in the ageing human brain. Nature (2025). https://doi.org/10.1038/s41586-025-09435-8

Image Credits: AI Generated