Cellular enlargement - A new hallmark of aging?

Spatially Resolved Single-Cell Morphometry of Benign Breast Disease Biopsy Images Uncovers Quantitative Cytomorphometric Features Predictive of Subsequent Invasive Breast Cancer Risk

Currently, benign breast disease (BBD) pathologic classification and invasive breast cancer (BC) risk assessment are based on qualitative epithelial changes, with limited utility for BC risk stratification for women with lower-risk category BBD (ie, nonproliferative disease [NPD] and proliferative disease without atypia [PDWA]). Here, machine learning-based single-cell morphometry was used to characterize quantitative changes in epithelial nuclear morphology that reflect functional/structural decline (ie, increasing nuclear size, assessed as epithelial nuclear area and nuclear perimeter), altered DNA chromatin content (ie, increasing nuclear chromasia), and increased cellular crowding/proliferation (ie, increasing nuclear contour irregularity). Cytomorphologic changes reflecting chronic stromal inflammation were assessed using stromal cellular density. Data and pathology materials were obtained from a case-control study (n = 972) nested within a cohort of 15,395 women diagnosed with BBD at Kaiser Permanente Northwest (1971-2012). Odds ratios (ORs) and 95% confidence intervals (CIs) for associations of cytomorphometric features with risk of subsequent BC were assessed using multivariable logistic regression. More than 55 million epithelial and 37 million stromal cells were profiled across 972 BBD images. Cytomorphometric features were individually predictive of subsequent BC risk, independently of BBD histologic classification. However, cytomorphometric features of epithelial functional/structural decline were statistically significantly predictive of low-grade but not high-grade BC following PDWA (OR for low-grade BC per 1-SD increase in nuclear area and nuclear perimeter, 2.10; 95% CI, 1.26-3.49, and 2.22; 95% CI, 1.30-3.78, respectively), whereas stromal inflammation was predictive of high-grade but not low-grade BC following NPD (OR for high-grade BC per 1-SD increase in stromal cellular density, 1.53; 95% CI, 1.13-2.08). Associations of nuclear chromasia and nuclear contour irregularity with subsequent tumor grade were context specific, with both features predicting low-grade BC risk following PDWA (OR per 1-SD, 1.58; 95% CI, 1.06-2.35, and 2.21; 95% CI, 1.25-3.91, for nuclear chromasia and nuclear contour irregularity, respectively) and high-grade BC following NPD (OR per 1-SD, 1.47; 95% CI, 1.11-1.96, and 1.29; 95% CI, 1.00-1.70, for nuclear chromasia and nuclear contour irregularity, respectively). The results indicate that cytomorphometric features on BBD hematoxylin-eosin-stained images might help to refine BC risk estimation and potentially inform BC risk reduction strategies for BBD patients, particularly those currently designated as low risk.

scCamAge: A context-aware prediction engine for cellular age, aging-associated bioactivities, and morphometrics

Current deep-learning-based image-analysis solutions exhibit limitations in holistically capturing spatiotemporal cellular changes, particularly during aging. We present scCamAge, an advanced context-aware multimodal prediction engine that co-leverages image-based cellular spatiotemporal features at single-cell resolution alongside cellular morphometrics and aging-associated bioactivities such as genomic instability, mitochondrial dysfunction, vacuolar dynamics, reactive oxygen species levels, and epigenetic and proteasomal dysfunctions. scCamAge employed heterogeneous datasets comprising ∼1 million single yeast cells and was validated using pro-longevity drugs, genetic mutants, and stress-induced models. scCamAge also predicted a pro-longevity response in yeast cells under iterative thermal stress, confirmed using integrative omics analyses. Interestingly, scCamAge, trained solely on yeast images, without additional learning, surpasses generic models in predicting chemical and replication-induced senescence in human fibroblasts, indicating evolutionary conservation of aging-related morphometrics. Finally, we enhanced the generalizability of scCamAge by retraining it on human fibroblast senescence datasets, which improved its ability to predict senescent cells.

Cell enlargement modulated by GATA4 and YAP instructs the senescence-associated secretory phenotype

Dynamic changes in cell size are associated with development and pathological conditions, including aging. Although cell enlargement is a prominent morphological feature of cellular senescence, its functional implications are unknown; moreover, how senescent cells maintain their enlargement state is less understood. Here we show that an extensive remodeling of actin cytoskeleton is necessary for establishing senescence-associated cell enlargement and pro-inflammatory senescence-associated secretory phenotype (SASP). This remodeling is attributed to a balancing act between the SASP regulator GATA4 and the mechanosensor YAP on the expression of the Rho family of GTPase RHOU. Genetic or pharmacological interventions that reduce cell enlargement attenuate SASP with minimal effect on senescence growth arrest. Mechanistically, actin cytoskeleton remodeling couples cell enlargement to the nuclear localization of GATA4 and NF-κB via the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex. RhoU protein accumulates in mouse adipose tissue under senescence-inducing conditions. Furthermore, RHOU expression correlates with SASP expression in adipose tissue during human aging. Thus, our study highlights an unexpected instructive role of cell enlargement in modulating the SASP and reveals a mechanical branch in the senescence regulatory network.

Raman Spectroscopy in Cellular and Tissue Aging Research

The establishment of various molecular, physiological, and genetic markers for cellular senescence and aging-associated conditions has progressed the aging study. To identify such markers, a combination of optical, proteomic-, and sequencing-based tools is primarily used, often accompanying extrinsic labels. Yet, the tools for clinical detection at the molecular, cellular, and tissue levels are still lacking which profoundly hinders advancements in the specific detection and timely prevention of aging-related diseases and pathologies. Raman spectroscopy, with its capability for rapid, label-free, and non-invasive analysis of molecular compositions and alterations in aging cells and tissues, holds considerable promise for in vivo applications. In this review, we present recent advancements in the application of Raman spectroscopy to the study of aging in cells and tissues. We explore the use of Raman spectroscopy and related techniques for detecting cellular aging and senescence, focusing on the molecular alterations that accompany these processes. Subsequently, we provide a review of the application of Raman spectroscopy in identifying aging-related changes in various molecules within tissues and organs.

Studying Cellular Senescence Using the Model Organism Drosophila melanogaster

Cellular senescence, a complex biological process characterized by irreversible cell cycle arrest, contributes significantly to the development and progression of aging and of age-related diseases. Studying cellular senescence in vivo can be challenging due to the high heterogeneity and dynamic nature of senescent cells. Recently, Drosophila melanogaster has emerged as a powerful model organism for studying aging and cellular senescence due to its tractability and short lifespan, as well as due to the conservation of age-related genes and of key age-related pathways with mammals. Consequently, several research studies have utilized Drosophila to investigate the cellular mechanisms and pathways implicated in cellular senescence. Herein, we provide an overview of the assays that can be applied to study the different features of senescent cells in D. melanogaster tissues, highlighting the benefits of this model in aging research. We also emphasize the importance of selecting appropriate biomarkers for the identification of senescent cells, and the need for further understanding of the aging process including a more accurate identification and detection of senescent cells at the organismal level; a far more complex process as compared to single cells.

Eukaryotic cell size regulation and its implications for cellular function and dysfunction

Depending on cell type, environmental inputs, and disease, the cells in the human body can have widely different sizes. In recent years, it has become clear that cell size is a major regulator of cell function. However, we are only beginning to understand how the optimization of cell function determines a given cell's optimal size. Here, we review currently known size control strategies of eukaryotic cells and the intricate link of cell size to intracellular biomolecular scaling, organelle homeostasis, and cell cycle progression. We detail the cell size-dependent regulation of early development and the impact of cell size on cell differentiation. Given the importance of cell size for normal cellular physiology, cell size control must account for changing environmental conditions. We describe how cells sense environmental stimuli, such as nutrient availability, and accordingly adapt their size by regulating cell growth and cell cycle progression. Moreover, we discuss the correlation of pathological states with misregulation of cell size and how for a long time this was considered a downstream consequence of cellular dysfunction. We review newer studies that reveal a reversed causality, with misregulated cell size leading to pathophysiological phenotypes such as senescence and aging. In summary, we highlight the important roles of cell size in cellular function and dysfunction, which could have major implications for both diagnostics and treatment in the clinic.

Virtually identical does not mean exactly identical: Discrepancy in energy metabolism between glucose and fructose fermentation influences the reproductive potential of yeast cells

The physiological efficiency of cells largely depends on the possibility of metabolic adaptations to changing conditions, especially on the availability of nutrients. Central carbon metabolism has an essential role in cellular function. In most cells is based on glucose, which is the primary energy source, provides the carbon skeleton for the biosynthesis of important cell macromolecules, and acts as a signaling molecule. The metabolic flux between pathways of carbon metabolism such as glycolysis, pentose phosphate pathway, and mitochondrial oxidative phosphorylation is dynamically adjusted by specific cellular economics responding to extracellular conditions and intracellular demands. Using Saccharomyces cerevisiae yeast cells and potentially similar fermentable carbon sources i.e. glucose and fructose we analyzed the parameters concerning the metabolic status of the cells and connected with them alteration in cell reproductive potential. Those parameters were related to the specific metabolic network: the hexose uptake - glycolysis and activity of the cAMP/PKA pathway - pentose phosphate pathway and biosynthetic capacities - the oxidative respiration and energy generation. The results showed that yeast cells growing in a fructose medium slightly increased metabolism redirection toward respiratory activity, which decreased pentose phosphate pathway activity and cellular biosynthetic capabilities. These differences between the fermentative metabolism of glucose and fructose, lead to long-term effects, manifested by changes in the maximum reproductive potential of cells.

Too big not to fail: emerging evidence for size-induced senescence

Cellular senescence refers to a permanent and stable state of cell cycle exit. This process plays an important role in many cellular functions, including tumor suppression. It was first noted that senescence is associated with increased cell size in the early 1960s; however, how this contributes to permanent cell cycle exit was poorly understood until recently. In this review, we discuss new findings that identify increased cell size as not only a consequence but also a cause of permanent cell cycle exit. We highlight recent insights into how increased cell size alters normal cellular physiology and creates homeostatic imbalances that contribute to senescence induction. Finally, we focus on the potential clinical implications of these findings in the context of cell cycle arrest-causing cancer therapeutics and speculate on how tumor cell size changes may impact outcomes in patients treated with these drugs.

The search for CDK4/6 inhibitor biomarkers has been hampered by inappropriate proliferation assays

CDK4/6 inhibitors are effective at treating advanced HR+ /HER2- breast cancer, however biomarkers that can predict response are urgently needed. We demonstrate here that previous large-scale screens designed to identify which tumour types or genotypes are most sensitive to CDK4/6 inhibitors have misrepresented the responsive cell lines because of a reliance on metabolic proliferation assays. CDK4/6-inhibited cells arrest in G1 but continue to grow in size, thereby producing more mitochondria. We show that this growth obscures the arrest using ATP-based proliferation assays but not if DNA-based assays are used instead. Furthermore, lymphoma lines, previously identified as the most sensitive, simply appear to respond the best using ATP-based assays because they fail to overgrow during the G1 arrest. Similarly, the CDK4/6 inhibitor abemaciclib appears to inhibit proliferation better than palbociclib because it also restricts cellular overgrowth through off-target effects. DepMap analysis of screening data using reliable assay types, demonstrates that palbociclib-sensitive cell types are also sensitive to Cyclin D1, CDK4 and CDK6 knockout/knockdown, whereas the palbociclib-resistant lines are sensitive to Cyclin E1, CDK2 and SKP2 knockout/knockdown. Potential biomarkers of palbociclib-sensitive cells are increased expression of CCND1 and RB1, and reduced expression of CCNE1 and CDKN2A. Probing DepMap with similar data from metabolic assays fails to reveal these associations. Together, this demonstrates why CDK4/6 inhibitors, and any other anti-cancer drugs that arrest the cell cycle but permit continued cell growth, must now be re-screened against a wide-range of cell types using an appropriate proliferation assay. This would help to better inform clinical trials and to identify much needed biomarkers of response.

Partial cellular reprogramming: A deep dive into an emerging rejuvenation technology

Aging and age-associated disease are a major medical and societal burden in need of effective treatments. Cellular reprogramming is a biological process capable of modulating cell fate and cellular age. Harnessing the rejuvenating benefits without altering cell identity via partial cellular reprogramming has emerged as a novel translational strategy with therapeutic potential and strong commercial interests. Here, we explore the aging-related benefits of partial cellular reprogramming while examining limitations and future directions for the field.

The hallmarks of aging as a conceptual framework for health and longevity research

The inexorability of the aging process has sparked the curiosity of human beings since ancient times. However, despite this interest and the extraordinary scientific advances in the field, the complexity of the process has hampered its comprehension. In this context, The Hallmarks of Aging were defined in 2013 with the aim of establishing an organized, systematic and integrative view of this topic, which would serve as a conceptual framework for aging research. Ten years later and promoted by the progress in the area, an updated version included three new hallmarks while maintaining the original scope. The aim of this review is to determine to what extent The Hallmarks of Aging achieved the purpose that gave rise to them. For this aim, we have reviewed the literature citing any of the two versions of The Hallmarks of Aging and conclude that they have served as a conceptual framework not only for aging research but also for related areas of knowledge. Finally, this review discusses the new candidates to become part of the Hallmarks list, analyzing the evidence that supports whether they should or should not be incorporated.

Cellular Senescence Program is Sensitive to Physical Differences in Polymeric Tissue Scaffolds

A typical cellular senescence program involves exposing cells to DNA-damaging agents such as ionization radiation or chemotherapeutic drugs, which cause multipronged changes, including increased cell size and volume, the onset of enhanced oxidative stress, and inflammation. In the present study, we examined if the senescence onset decision is sensitive to the design, porosity, and architecture of the substrate. To address this, we generated a library of polymeric scaffolds widely used in tissue engineering of varied stiffness, architecture, and porosity. Using irradiated A549 lung cancer cells, we examined the differences between cellular responses in these 3D scaffold systems and observed that senescence onset is equally diminished. When compared to the two-dimensional (2D) culture formats, there were profound changes in cell size and senescence induction in three-dimensional (3D) scaffolds. We further establish that these observed differences in the senescence state can be attributed to the altered cell spreading and cellular interactions on these substrates. This study elucidates the role of scaffold architecture in the cellular senescence program.