Trends in Cell Biology

Merlin–YAP signaling: emerging mechanisms, functions, and therapeutic approaches The Hippo signaling pathway has a critical role in regulating tissue growth, development, and tumor suppression. Mutations in NF2, which encodes the tumor suppressor Merlin, disrupt Hippo signaling, causing aberrant activation of YAP/TAZ and contributing to diseases, such as cancer and developmental disorders. Recent studies have identified novel mechanisms by which biomolecular condensation and phosphoinositides regulate Merlin function in Hippo signaling. Furthermore, NF2 deficiency sensitizes cells to ferroptosis, a form of regulated cell death characterized by iron-dependent lipid peroxidation. In this review, I highlight the emerging roles of Merlin–YAP signaling in physiology and disease, focusing on its regulation through biomolecular condensates, its contribution to development and ferroptosis, and its implications for therapeutic interventions.

Merlin–YAP signaling: emerging mechanisms, functions, and therapeutic approaches

Roles of lysosomal small-molecule transporters in metabolism and signaling Lysosomes degrade damaged or unwanted cell/tissue components and recycle their building blocks through small-molecule transporters of the lysosomal membrane. They also act as signaling hubs that sense and signal internal cues, such as amino acids, to coordinate cell responses. Recently, the activity of several lysosomal metabolite transporters has been elucidated, bringing new insights into lysosomal functions. Cell biological and structural studies of lysosomal transporters have also highlighted their roles in recruiting signaling complexes to lysosomes and delineated how their substrates gate such hybrid transporter/receptor, or ‘transceptor’, function. In this review, we summarize recent progress in our understanding of lysosomal transporters, with a focus on the export of lysosomal degradation intermediates, the existence of lysosomal amino acid shuttles that regulate the redox state and pH of the lysosomal lumen, and the role of lysosomal transceptors in nutrient and immune signaling.

Roles of lysosomal small-molecule transporters in metabolism and signaling

The promiscuous ribosomal P-stalk: a new functional portrait The canonical role of the ribosome is to translate the genetic code into functional proteins. Recent discoveries, however, redefine the eukaryotic ribosome, as a regulatory hub, that senses cellular cues and transmits signals to downstream pathways. The P-stalk, an integral component of the ribosomal GTPase-associated center, once viewed as translational supporter, is now emerging as a key regulatory ribosomal module. It has recently been recognized as an activator of the integrated stress response, reshaping the Gcn1/Gcn20→Gcn2 axis into the new Gcn1/Gcn20/P-stalk→Gcn2 order. The P-stalk's structural plasticity allows also the ribosome to rewire gene expression in response to cellular demands, including cytokine response. In this review, an updated functional portrait of the P-stalk is presented, encompassing both ribosome-dependent and -independent activities.

The promiscuous ribosomal P-stalk: a new functional portrait

Phosphoinositide dynamics in virus-associated malignancies Virus-associated cancers, which account for ~15–20% of the global cancer burden, arise from infections with human oncoviruses. These viruses drive malignant transformation through diverse mechanisms but share common oncogenic features, including reprogramming host membrane signaling and trafficking. Such processes are tightly regulated by phosphoinositides (PPIn), essential organizers of membrane dynamics and signal transduction implicated in cancer development and progression. Oncoviruses exploit host PPIn metabolism to facilitate their replication and persistence, often leading to its dysregulation. In turn, this disruption can activate oncogenic signaling pathways that promote malignant transformation. In this review, we summarize how oncoviruses manipulate PPIn metabolism to sustain their life cycle and drive long-term interactions with host cells, ultimately contributing to tumorigenesis.

Phosphoinositide dynamics in virus-associated malignancies

Optimality as a framework for understanding developmental robustness Embryo growth, morphogenesis, and patterning are complex processes that coordinate between cellular dynamics, fate specification, and multiscale physical forces. Understanding how robustness in embryo development is achieved despite inherent heterogeneities in gene expression, cell properties, and tissue growth is a fundamental question. Although various feedback between gene expression, signaling, and cell and tissue mechanics have been uncovered to confer robustness on developmental systems, measuring variability and robustness from a quantitative perspective often remains challenging. Furthermore, cell fate plasticity, a key mechanism that can confer robustness, is lacking in many developing tissues. This review highlights how recent technological and conceptual advances in quantitative approaches to biology help to overcome these bottlenecks, with a particular focus on how mechanochemical feedback, or alternatively, selectively tuned control parameters, ensure developmental robustness.

Optimality as a framework for understanding developmental robustness

Targeting the cell-cycle machinery for cancer therapy The cell cycle is governed by tightly regulated checkpoints and proteogenomic oscillations that ensure genomic fidelity during cell proliferation. Dysregulation of the cell cycle can drive oncogenic transformation, and this positions it as a pivotal target in precision oncology. Recent advances reveal how proteomic and post-translational dynamics orchestrate cell-cycle phase transitions that are aberrantly disrupted in cancers. Therapeutic targeting of the CDK4/6 represents a cornerstone of cancer therapy, but resistance mechanisms limit its clinical efficacy. Emerging strategies such as targeted protein degradation, synthetic lethality, and combination immunotherapies further expand the therapeutic window. These innovations, coupled with biomarker-driven precision medicine, exploit cell-cycle vulnerabilities and transform them into an active tool to combat human cancers more effectively. This review highlights emerging mechanistic insights underlying tumorigenesis driven by an aberrant cell cycle and proposes potential therapeutics aimed at cell-cycle machinery-relevant targets.

Targeting the cell-cycle machinery for cancer therapy

Organelle-specific signaling of cGAS–STING Innate immune sensing through cyclic GMP-AMP synthase (cGAS)–stimulator of interferon genes (STING) surveils cytosolic DNA from invading pathogens or damaged organelles and initiates a spectrum of immune responses. It is well established that upon 2′3′-cyclic GMP-AMP (cGAMP) binding, STING exits the endoplasmic reticulum (ER), traverses the Golgi to trigger interferon programs, and finally reaches lysosomes for signal resolution through degradation, revealing a tightly choreographed itinerary for cytokine-driven immunity. However, emerging studies reveal additional layers of spatiotemporal complexity: ER-resident STING tunes in messenger RNA translation and Ca2+ efflux, Golgi-localized STING functions as a proton channel that initiates H+-dependent autophagy and transcription factor EB-directed programs for organelle homeostasis, and various mechanisms for metabolic remodeling and cell fate determination. This review synthesizes emerging organelle-specific mechanisms of cGAS–STING, delineates their roles in physiology and disease, and discusses how an organelle-centric perspective may inform selective, context-sensitive immunotherapies.

Organelle-specific signaling of cGAS–STING

What makes genes burst Genes burst. Instead of being monotonously transcribed by a steady stream of RNA polymerases, active genes undergo transient and random pulses of transcription that are referred to as gene bursting. This property is ubiquitous and evolutionarily conserved from bacteria to humans, and reflects the inherent stochastic nature of most biological processes. The frequency and duration of gene busting events varies greatly between genes and is now recognized to be controlled by an intricate interplay between transcription factors, chromatin features, and the transcription machinery. Recent findings also point to proximal regulation of bursting by epigenetic chromatin states, a novel role of non-histone modifications, and of distal control of bursting patterns by enhancers. Uncovering the regulatory mechanisms of gene bursting sheds light on how cells maintain a diverse range of gene-specific expression by modulating the different kinetic parameters of bursting.

What makes genes burst

Understanding human embryogenesis by building programmable stem cell-based models

Polysome sorting controls mRNA localization and protein fate RNA localization and local translation are widespread phenomena that play key roles in a plethora of cellular processes ranging from embryo patterning to general cellular functions. The traditional paradigm assigns localization elements to cis-acting RNA sequences which assemble into complexes that regulate mRNA transport and translation, and the mRNA is generally transported while remaining translationally silent. However, recent evidence has shown that the nascent protein can also play an essential role in RNA localization and can enable polysomes to control their own transport and be delivered where and when they are needed. Two such examples are reviewed: translation factories and centrosomal mRNAs. Their comparison highlights the key role of cotranslational interactions in the spatiotemporal control of protein synthesis and protein fate.

Polysome sorting controls mRNA localization and protein fate

Physiological aging in three dimensions Aging is characterized by progressive structural and functional decline, driven partially by epigenetic alterations. While changes in DNA methylation, histone modifications, and chromatin accessibility are well studied, the role of three-dimensional chromatin organization in aging remains underexplored. Advances in chromosome conformation capture technologies have revealed hierarchical chromatin structures, including compartments, topologically associating domains (TADs), and chromatin loops, which are crucial for gene regulation. Emerging evidence suggests that aging changes these structures, leading to altered gene expression and cellular dysfunction. This review summarizes recent findings on age-associated chromatin reorganization, highlighting its impact on transcription and nuclear architecture. It also compares the roles of 3D chromatin organization in aging and senescence, highlighting shared and distinct features in these biological contexts.

Physiological aging in three dimensions

TGF-β signaling as an organismal proteostasis regulator Various mechanisms act in a coordinated manner to maintain proteostasis in different cellular organelles. Nevertheless, with aging, certain proteins escape proteostasis surveillance, misfold, and aggregate. This process can lead to neurodegeneration. Despite the cellular nature of proteostasis, it is regulated by intertissue communication. How these intertissue signaling mechanisms coordinate proteostasis across the organism is largely obscure. Recent studies unveiled that the transforming growth factor (TGF)-β signaling cascade is an organismal proteostasis regulator. Here, we focus on the known roles of the TGF-β pathway as a coordinator of proteostasis and describe the messengers and biological activities that are controlled by this pathway. We also discuss open questions and highlight the potential clinical relevance of these discoveries.

TGF-β signaling as an organismal proteostasis regulator

The Wnt–NAD+ axis in cancer, aging, and tissue regeneration The intricate interplay between Wnt signaling and nicotinamide adenine dinucleotide (NAD+) biosynthesis has emerged as a crucial axis that influences aging and tissue regeneration. Wnt signaling, a key regulator of cellular proliferation, differentiation, and tissue homeostasis, intersects with NAD+ metabolism, a cornerstone of cellular energy balance and genomic stability. This relationship is mediated through shared regulatory pathways involving sirtuins, poly(ADP-ribose) polymerases (PARPs), and metabolic enzymes which are sensitive to cellular NAD+ levels. Dysregulation of either pathway is implicated in cancer, age-related decline, and impaired regenerative capacity. This review consolidates current knowledge of the Wnt–NAD+ axis and highlights its cooperative roles in maintaining tissue integrity and combating the effects of aging. Furthermore, it explores therapeutic approaches targeting this axis to restore tissue health and enhance the capacity for repair, thereby offering promising avenues for addressing age-associated pathologies.

The Wnt–NAD+ axis in cancer, aging, and tissue regeneration

Navigating AKT-ivity across cellular compartments Phosphoinositide (PIP)-mediated AKT signaling is essential for cellular homeostasis because it orchestrates crucial processes such as metabolism, survival, proliferation, and motility. Dysregulation of this pathway drives various pathologies, particularly cancer. Although cytosolic activation of AKT has been extensively studied, its emerging roles in the nucleus have gained attention over the past decade. The complexities of AKT compartmentalization and associated functional mechanisms remain largely unexplored. At the plasma membrane, AKT activation occurs at specialized microdomains and cell–cell junctions where it influences polarity, adhesion, and migration. In endosomes, PIPs coordinate intracellular trafficking and cytoskeletal organization with AKT signaling. Protein scaffolds refine AKT signal specificity by assembling complexes. In the nucleus, AKT interacts with the p53–PIP signalosome and specific kinases to regulate oncogenesis and chemoresistance. This review explores PIP-driven spatial regulation of AKT across cellular compartments, emphasizing its role in cellular responses and oncogenesis. Understanding AKT compartmentalization mechanisms provides valuable insights into cancer biology and novel therapeutic strategies.

Navigating AKT-ivity across cellular compartments

The role of nutrient stress in DNA damage Cells are constantly exposed to various stresses, including nutrient deprivation and genotoxic stress, which dynamically interact with cellular sensing pathways to influence metabolism, gene expression, and homeostasis. The integration of nutrient-sensing mechanisms and DNA damage response pathways is critical in cancer progression. While individual processes are well-characterized, their cross-regulatory mechanisms are just beginning to emerge. Deciphering the interplay between nutrient stress and DNA damage is crucial for elucidating the mechanisms underlying cellular responses to stress and developing therapeutic strategies for various diseases, including cancer. This review highlights the relationship between nutrient stress and DNA damage, especially its underlying sensing pathway and cell fate determination.

The role of nutrient stress in DNA damage

Is mitochondrial function at the heart of ribosome-related diseases? Defects in ribosomal machinery cause ribosomopathies such as Diamond Blackfan anemia, classically linked to impaired protein synthesis. However, emerging evidence places mitochondrial dysfunction as a critical downstream consequence of ribosomal insufficiency. Thus, is impaired energy metabolism, rather than translation alone, a key driver of ribosomopathies such as Diamond Blackfan anemia? This insight could reframe our understanding of disease mechanisms and could identify metabolic pathways as promising therapeutic targets.

Is mitochondrial function at the heart of ribosome-related diseases?

Special issue

Death by ribosome — new insights from Anna Constance Vind, Franklin Zhong & Simon Bekker-Jensen on how ribosomal dysfunction can drive cell death.
Read more: http://dlvr.it/TMVfKc

Special issue

Dynamic rRNA modifications as a source of ribosome heterogeneity — new insights from Ivan Milenkovic & Eva Maria Novoa.
A fresh perspective on how ribosomes diversify function through epitranscriptomic changes.
Read more: http://dlvr.it/TMSZ68

Special issue

Cell cycle regulation via the ribotoxic stress response — Connor McKenney & Sergi Regot uncover how ribosome damage impacts cell cycle control.
Read more: http://dlvr.it/TMQRqm

Decoding the language of PLK1 docking motifs and activation mechanisms Polo-like kinase 1 (PLK1) phosphorylates a plethora of different substrates to regulate key cell cycle processes that include, among others, mitotic entry, chromosome condensation, nuclear envelope breakdown, centrosome maturation, spindle assembly and chromosome biorientation, cytokinesis, and the deposition of the specialized centromere histone CENP-A. Addressing the exact spatial and temporal control of PLK1 activity in these processes and its dynamic interplay with protein phosphatases that counteract mitotic phosphorylation, most notably PP1 and PP2A, has proven especially puzzling. In this review, we focus on the main unknowns in the area of human PLK1 regulation, exploring more specifically an emerging concept that master docking sites, including newly discovered noncanonical motifs, trigger initial local activation of PLK1 that promotes subsequent localized spreading of phosphorylation.

Decoding the language of PLK1 docking motifs and activation mechanisms

Special issue

MDM4 exon skipping upon dysfunctional ribosome assembly - new findings from Jennifer Jansen & Matthias Dobbelstein reveal a surprising link between ribosome biogenesis and mRNA splicing.
Read more: http://dlvr.it/TMLvmY

NADH reductive stress drives metabolic reprogramming Cellular metabolism is intricately regulated by redox signaling, with the NADH/NAD+ couple serving as a central hub. Emerging evidence reveals that NADH reductive stress, marked by NADH accumulation, is not merely a passive byproduct of metabolic dysfunction but an active regulatory signal driving metabolic reprogramming. In this Review, we synthesize recent advances in understanding NADH reductive stress, including its origins, regulatory mechanism, and manipulation. We examine its broad impact on cellular metabolism, its interplay with oxidative and energy stress, and its pathogenic roles in a range of diseases. By integrating these findings, we propose NADH reductive stress as a master regulator for metabolic reprogramming and highlight new avenues for mechanistic exploration and therapeutic intervention.

NADH reductive stress drives metabolic reprogramming

Special issue

Celebrating 35 years of Trends in Cell Biology!
Explore our special anniversary issue spotlighting ribosomal dynamics and cellular homeostasis.
Dive into the latest insights: http://dlvr.it/TMHXH4

Lessons in longevity from blood stem cells under protein stress Blood stem cells are among the body’s longest-living cells despite being highly vulnerable to proteotoxic damage, which accelerates their aging. To maintain protein homeostasis (proteostasis), hematopoietic stem cells (HSCs) employ mechanisms such as reduced translation rates, high chaperone activity, autophagy, and selective protein degradation. These strategies mitigate protein misfolding, maintain quiescence, and preserve regenerative potential. Disruptions in proteostasis can lead to the elimination of impaired HSCs through differentiation or apoptosis, ensuring the integrity of the stem cell pool. Due to the systemic impact of the blood on aging and its experimental and clinical accessibility, investigating HSC proteostasis provides insights into longevity and potential therapeutic strategies. This review examines emerging mechanistic links between proteostasis and HSC fate, concluding with unresolved questions and challenges of the current research.

Lessons in longevity from blood stem cells under protein stress

ATRX loss induces lineage plasticity and squamous-like phenotype to promote colorectal cancer metastasis Colorectal cancer (CRC) metastasis is driven by phenotypic plasticity beyond classic epithelial–mesenchymal transition (EMT), including non-canonical lineages such as squamous-like phenotypes. Their regulatory mechanisms and clinical significance remain unclear. In the current issue of Nature, Cammareri et al. identified ATRX loss as a driver of multilineage plasticity, including squamous-like characteristics, linked to increased metastasis and poor clinical outcomes in CRC.

ATRX loss induces lineage plasticity and squamous-like phenotype to promote colorectal cancer metastasis

Science in Mexico: a rising force amid adversity Despite its economic and population status, Mexico’s scientific output remains under 1% of global production because of low spending on science. Yet, additional challenges, including over-reliance on expensive imported technology, brain drain, and limited private sector investment, further hinder its progress. Nonetheless, significant opportunities exist, such as fostering local biotechnology, enhancing policy continuity, and leveraging new leadership to boost scientific growth. Although focused on Mexico, these insights hold relevance for the broader region of Latin America, a region that shares vast untapped scientific potential.

Science in Mexico: a rising force amid adversity

Endosome–ER contact sites in phagophore formation Autophagy is a crucial ‘self-eating’ mechanism used by eukaryotic cells to degrade and recycle cytosolic materials. A recent study by Da Graça et al. reports that the dynamic mobilization of endosome–endoplasmic reticulum (ER) contact sites (EERCS) in response to starvation creates a confined environment that facilitates Ca2+-dependent phagophore biogenesis.

Endosome–ER contact sites in phagophore formation

Unlocking Latin America´s scientific potential: challenges and opportunities in a globalized world Latin America shows increasing scientific potential, with a dedicated and creative research community, driven by resilience and adaptability. However, limited funding, restricted access to cutting-edge technology, bureaucratic barriers, and constantly changing scientific policies continue to hinder its full integration into the international scientific ecosystem. Latin American scientists also suffer from limitations in their visibility on the global stage, often leading to exclusion. Despite these challenges, many success cases in the region highlight how strategic actions based on planned and sustained investments, international collaborations, and a relevant scientific policy positively impact scientific progress. Through this path, Latin America may not only overcome existing barriers but also position itself as a fundamental player in the scientific stage.

Unlocking Latin America´s scientific potential: challenges and opportunities in a globalized world

Stem-like cells at the center of CD4 T cell differentiation CD4 T cells orchestrate immune responses through differentiation into specialized helper subsets. Traditionally, CD4 T cell differentiation is described as a linear process in which naïve CD4 T cells commit to distinct effector lineages upon activation. However, growing evidence challenging this paradigm has provoked considerable debate about CD4 T cell plasticity. This review describes the emerging concept of stem-like CD4 T cells and how they update our understanding of the fundamental mechanisms that regulate CD4 T cell differentiation. We discuss how stem-like CD4 T cells play a crucial role as precursor cells to distinct effector subsets and explore their implications in cancer, infections, and autoimmunity. Finally, we address how stem-like CD4 T cells might resolve long-standing questions about CD4 T cell plasticity, and propose alternative differentiation models that incorporate this population in chronic diseases.

Stem-like cells at the center of CD4 T cell differentiation

Communicating science in Latin America: insights, challenges, and future directions This article reviews public science communication (SC) in Latin America, highlighting advances and challenges. It emphasizes the need to foster inclusive policies, interdisciplinary approaches, and effective evaluation to enhance public engagement, address social inequalities, and foster informed decision-making. Improving this field would strengthen science–society relationships, benefiting both professional communicators and scientific communities.

Communicating science in Latin America: insights, challenges, and future directions