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How Automation and AI Are Transforming Organoid Research

The life sciences are in the midst of a crucial shift, driven by the emergence of organoid-based models and the power of automation. Organoids—three-dimensional cell cultures that mimic human tissue architecture and function—are enabling researchers to ask and answer questions that were once beyond reach. Paired with advances in automation, robotics, and artificial intelligence (AI), these models are transforming drug discovery and preclinical testing, offering a more human-relevant alternative to outdated 2D cell cultures and animal models. This revolution is reshaping the pharmaceutical industry, while also holding the potential to accelerate progress in personalized medicine.

Beyond 2D: The Rise of Organoids

For decades, preclinical research has relied on 2D cell cultures, single-cell-type 3D spheroid models, and animal models, despite their limitations in replicating human biology. Organoids, which are derived from stem cells, offer a more accurate representation of human tissues, recapitulating complex biological processes such as organ-specific functionality and cellular interactions. These miniature self-organizing biological systems are being used to model diseases, test drug efficacy and toxicity, and even explore regenerative medicine.

Organ-on-a-chip technology replicates decades of human aging in just four days

Over one billion people worldwide are over 60, and the population is projected to more than double by 2050. But as more people live into their 60s, 70s, and 80s, health care systems across the globe may face new challenges as they attempt to manage associated increases in age-related disease.

Metabolic biologist Andreas Stahl and preeminent longevity researcher Irina Conboy argue that the graying of the global population underscores the need to understand aging as a biological process, and how it might be slowed or reversed. Longevity therapeutics, however, are expensive to develop, and the lack of rapid, reliable tools to study human aging can make it difficult to test these next-generation therapies. While animal models can provide important data, there are often many caveats when applying those findings to human biology during trials.

“Over $130 billion is spent on drug development each year in the United States, but over 90% end up failing in clinical trials,” explained Stahl, the Ruth Okey Professor in the Department of Metabolic Biology and Nutrition (MBN) and a member of the California Institute for Quantitative Biosciences at UC Berkeley (QB3-Berkeley). “Pharmaceutical developers and regulators such as the US Food and Drug Administration are increasingly realizing that we need to change our drug development pipeline and make it more relevant to human biology.”

Negative social ties as emerging risk factors for accelerated aging, inflammation, and multimorbidity

Negative social ties, or “hasslers,” are pervasive yet understudied components of social networks that may accelerate biological aging and morbidity. Using ego-centric network data and DNA methylation-based biological aging clocks (i.e., DunedinPACE and age-accelerated GrimAge2) from saliva from a state representative probability sample in Indiana, we examine how negative social ties are associated with accelerated biological aging and a broad range of health outcomes, including inflammation and multimorbidity. Negative relationships are not rare within close relationships, as nearly 30% of individuals report having at least one hassler in their network. These hasslers tend to occupy peripheral network positions and are more likely to be connected through weak, uniplex ties. Importantly, exposure to negative social ties follows patterns of social and health vulnerability, with women, daily smokers, people in poorer health, and those with adverse childhood experiences more likely to report having hasslers in their networks. Having more hasslers is associated with accelerated biological aging in both rate and cumulative burden: Each additional hassler corresponds to approximately 1.5% faster pace of aging and roughly 9 mo older biological age. Moreover, not all hasslers exert the same influence; kin and nonkin hasslers show detrimental associations, whereas spouse hasslers do not. Finally, a greater number of hasslers is associated with multiple adverse health outcomes beyond epigenetic aging. These findings together highlight the critical role of negative social ties in biological aging as chronic stressors and the need for interventions that reduce harmful social exposures to promote healthier aging trajectories.

The longevity effects of reduced IGF-1 signaling depend on the stability of the mitochondrial genome

This insight has major implications for the development of antiaging therapies. First, they suggest that mtDNA integrity is not simply one of the many hallmarks of aging, but rather the foundation upon which others are built. And when that platform is broken, downstream hallmarks such as proteostasis or DNA repair cannot be engaged by typical means. Second, it suggests that interventions that target nutrient-sensing pathways may fail, or even backfire, when applied to organisms or tissues with high levels of mitochondrial damage. Hence, the next generation of geroprotective treatments must be tested in diverse models of aging, including those that combine multiple hallmarks, to better understand the scope and boundaries of their efficacy. Last, the efficacy of those treatments could be amplified by measures that improve the stability of the mitochondrial genome. While a reduction in IGF-1 signaling did not alter the frequency of mutations in WT or PolgD257A mice, it did slow the pace with which they reached homoplasmy. Thus, although it may not be possible today to reduce mitochondrial mutagenesis in human cells, our data show that it may already be possible to curtail the impact of mtDNA mutations on mammalian health span by slowing their clonal expansion in nondividing cells, the cells that are most sensitive to metabolic dysfunction.

While the precise mechanism by which Pappa influences clonal expansion of mtDNA mutations remains uncertain, several plausible explanations can be proposed. In the absence of cell division (the major driver for homoplasmy in dividing cells), the progression of mtDNA mutations toward homoplasmy is primarily driven by random genetic drift, the rate of mtDNA replication, and mitochondrial quality control. Thus, it is likely that loss of Pappa influences one of these three processes. Loss of Pappa may either reduce the rate of random genetic drift (potentially by changing mitochondrial fusion and fission or the spatial segregation of semi-isolated pockets of mtDNA), reduce the rate of mtDNA replication (less replication lowers the chance that a mutant mtDNA molecule expands enough to reach homoplasmy), or improve mitochondrial quality control by degrading mitochondria with mutant mtDNA molecules. It will be important to distinguish between these possibilities in future work to clear the way for novel interventions aimed at curbing the impact of mtDNA mutations on human health.

Regardless of the mechanism, these findings provide a compelling example of how the interplay between distinct hallmarks of the aging process can fundamentally alter the outcome of otherwise beneficial interventions. They reveal that the efficacy of antiaging strategies such as IGF-1 suppression is not absolute but context dependent. They are contingent on the integrity of underlying systems, including proteostasis and DNA repair. Without an intact mitochondrial genome, these pathways cannot be engaged, indicating that mtDNA integrity is required for these critical antiaging pathways. More broadly, our results underscore the need for a more integrated model of aging, one that considers not only individual pathways but also their interactions, hierarchies, and points of failure. By mapping these interactions, we can better anticipate the limitations of existing interventions and design next-generation therapies that are robust to the complex biology of aged tissues. In this light, strategies that target the expansion of mtDNA mutations, rather than their origin, may offer a powerful new axis for preserving tissue function and extending health span, even when the underlying genomic damage cannot be undone.

Frontiers: Background:

Chlorogenic acid (CGA) and taurine are well-known antioxidant compounds reported to reduce skin cellular senescence. However, the biological mechanisms underlying their skin-protective effects remain unclear.

Methods:

In this study, we conducted transcriptome-wide RNA sequencing to profile gene expression changes in human epidermal keratinocytes, melanocytes, and fibroblasts following treatment with CGA, taurine, or their combination. To identify aging-related genes, we integrated evidence from aging databases, perceived-age GWAS, enrichment in aging-related gene ontology and pathways, and drug-gene interaction annotations. Validation of representative genes was performed using quantitative real-time PCR.

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