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Rocha, S.

Publications and source records attributed to Rocha, S..

At least 19 recordsLinked to original sources

Letting go to hold on: loss of CCM2 disrupts endothelial force balance in cerebral cavernous malformations

Cerebral cavernous malformations (CCM) are vascular lesions characterized by impaired endothelial integrity and altered cell-cell and cell-matrix interactions. While endothelial contractility and tractions have been implicated in CCM, how these forces are transmitted and coordinated across adhesion systems remains unknown. Here, we combined genetically encoded FRET-based molecular tension sensors of vinculin and VE-cadherin with quantitative analysis of adhesion organization to dissect this force balance in CCM2-deficient endothelial monolayers. We found that CCM2 loss redistributes molecular forces, partially through ROCK-dependent contractility, across endothelial adhesions, shifting mechanical engagement from cell-cell junctions toward the cell-matrix interface. Matrix stiffness further amplifies this imbalance, as healthy endothelial cells maintain the balance between cell-cell and cell-matrix adhesions by reinforcing both in response to stiffening, whereas CCM2-deficient cells preferentially reinforce the cell-matrix interface. These findings suggest that CCM-associated matrix remodeling could reinforce an already altered mechanical state, establishing a potential feed-forward interaction between endothelial force transmission and the extracellular environment. More broadly, our results identify the CCM complex as a molecular hub controlling force balance in response to the cell mechanical environment and establish a combined tension sensing and morphology-based imaging platform for studying adhesion mechanobiology.

biophysics↗

Endothelial gain of PIEZO/TRPV mechanosensors drives cavernous malformations

Vascular disease often begins as a failure to read mechanical force. Cerebral cavernous malformations (CCMs) are leaky, brain-invading capillary clusters that cause stroke and seizures and arise from endothelial loss of the CCM complex. They form exclusively in low-flow vessels but existing models cannot explain this selectivity. We previously established that CCM-mutant endothelium inverts its adhesive balance, weakening cell-cell junctions while building matrix-degrading adhesions. The mechanosensors imposing this switch are unknown. Here we show that the mechanosensitive Ca2+ channels PIEZO1, TRPV2 and TRPV4 are overexpressed in the endothelium of CCM lesions in a 42-patient cohort, and that lesion volume scales with their expression level. Mechanistically, PIEZO1 partners with TRPV4 to destabilise cell-cell junctions and with TRPV2 to reinforce cell-matrix adhesions; silencing TRPV4 restores junctional integrity and abolishes KLF4 induction, whereas silencing TRPV2 or inhibition with tranilast abolishes matrix degradation and invasion. In vivo, trpv4 knockdown or inhibition with GSK2798745 restores atrioventricular canal morphogenesis in ccm2-mutant zebrafish. Gain of mechanosensory channel function is thus a causal step in CCM pathogenesis, upstream of the KLF program. Combined therapeutic targeting of TRPV2 and TRPV4 with inhibitors validated in humans offers a route to therapy.

cell biology↗

Prenatal exposure to PFAS and multimodal structural brain development across childhood

BackgroundPer- and polyfluoroalkyl substances (PFAS) are ubiquitous environmental pollutants that are posited to be neurotoxic to the developing brain; however, the impact of prenatal exposure to PFAS -- particularly to newer, short-chain PFAS -- on brain development across childhood is unclear. MethodsConcentrations of 9 PFAS were quantified in cord blood plasma of 459 infants who later participated in structural and diffusion magnetic resonance imaging (MRI) at ages 4.5, 6, 7.5, and 10.5 years, providing estimates of regional cortical thickness and surface area, subcortical volumes, and fractional anisotropy (FA) of key white matter tracts. Longitudinal mixed effect models estimated associations of PFAS with age 4.5 brain metrics and their developmental trajectories across childhood. ResultsHigher concentrations of long-chain PFAS (PFNA, PFHxS, PFDA) in cord blood were associated with lower surface area of the right paracentral lobule at age 4.5. PFHpA was associated with faster surface area growth in the left rostral anterior cingulate and slower growth in the right caudal middle frontal gyrus from 4.5 to 10.5 years. The short-chain compound PFBS was linked with greater FA in 17 of 27 white matter tracts at 4.5 years; those associations attenuated with age. Finally, PFOA was associated with lower FA in 6 tracts at 4.5 years. ConclusionsPrenatal exposure to PFAS was associated with altered development of frontal and paracentral regions and of white matter microstructure. These findings highlight the need for further research examining the long-term effects of prenatal exposure to PFAS on childrens neurodevelopment.

neuroscience↗

Synthetic Fibrous Hydrogels as Minimal Systems to Modulate Cell Migration Modes in 3D

Cell migration in three-dimensional (3D) environments is highly plastic and regulated by extracellular matrix (ECM) cues. Engineered biomaterials provide controllable platforms to investigate how specific matrix signals regulate cell behavior in 3D, yet how defined biochemical signals control migration modes remain unclear. Here, we present tunable fibrous polyisocyanide (PIC) hydrogels functionalized with integrin-binding RGD peptides, cadherin-mimetic HAVDI peptides, or no ligands to direct mesenchymal, hybrid, or amoeboid-like migration of human adipose-derived stem cells without altering matrix mechanics. Using live-cell tracking, 3D displacement microscopy, matrix remodeling analysis, and YAP nuclear localization, we show that ligand identity governs adhesion organization, force transmission, and mechanotransduction. RGD-functionalized matrices promote {beta}1-integrin clustering, extensive matrix remodeling, strong YAP activation and upregulation of migration-related genes. In contrast, non-adhesive matrices limit adhesion formation, resulting in weak force transmission and amoeboid-like behavior. HAVDI-functionalized matrices induce cadherin clustering and heterogeneous cellular responses, indicating that a hybrid migration mode arises from adhesion organization rather than a distinct transcriptional program. Together, these findings demonstrate that ligand identity alone is sufficient to program migration mode in a force-responsive 3D matrix and provide a versatile platform to dissect cell-matrix interactions in complex environments. Statement of significanceO_LICell migration in tissues is highly adaptable, yet precise control of migration modes in defined 3D biomaterials remains challenging. C_LIO_LIWe introduce fibrous PIC hydrogels presenting RGD, HAVDI, or no adhesive ligands to bias human stem cells toward mesenchymal-like, hybrid, or amoeboid-like migration states. C_LIO_LIBy linking ligand identity to adhesion organization, matrix remodeling, YAP mechanotransduction, and gene expression, this work provides a minimal platform to dissect and engineer 3D cell-matrix interactions C_LI

biophysics↗

When lysosomes persist: resolving the proton-sponge paradox in nanoparticle-based intracellular delivery

Proton-sponge-active polymers are widely used in nanomedicine to enhance intracellular delivery, yet the mechanism by which they promote cytosolic release of therapeutic cargo remains under debate. Whether these materials drive complete endolysosomal escape or instead alter lysosomal integrity without full nanoparticle release remains unclear. Here we show that polyethylene imine (PEI), a prototypical proton sponge active polymer, induces lysosomal membrane destabilization rather than full nanoparticle escape. Using PEI-coated mesoporous silica nanoparticles as a model delivery system, we show that PEI promotes cytosolic release of small-molecule cargo while nanoparticles remain confined within membrane-enclosed LAMP1-positive compartments. This behaviour arises from the combination of partial lysosomal membrane permeabilization and lysosomal deacidification, which together enable cargo leakage while impairing detection of lysosomes by pH-dependent probes. Our results resolve a long-standing ambiguity in the nanomedicine field and provide a revised mechanistic framework for interpreting endolysosomal escape in intracellular delivery. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/721565v2_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@74b98org.highwire.dtl.DTLVardef@f405eborg.highwire.dtl.DTLVardef@b0a276org.highwire.dtl.DTLVardef@79f154_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

Phosphorylation at S345 Converts HIF-2α from a Transcription Factor to an RNA binding protein

Oxygen sensing and adaptation are vital for metazoan survival. At the cellular level the response to hypoxia is characterised by a switch in transcriptional programming, primarily mediated by hypoxia-inducible factors (HIFs). HIFs comprise an obligatory heterodimer between an oxygen-sensitive HIF- subunit and an oxygen-insensitive HIF-1{beta} subunit, which together regulate gene expression in response to hypoxia. Among the three HIF- proteins in vertebrates (HIF-1, HIF-2, and HIF-3), post-translational modifications (PTMs) play a crucial role in modulating their stability, localisation, and activity. While many modifications have been investigated on HIF-1, our knowledge of HIF-2 regulation is very limited. Here, we investigated the function of the recently identified HIF-2 S345 phosphorylation site and demonstrate that this disrupts the interaction between HIF-2 and HIF-1{beta}, thereby silencing the HIF-2 transcriptional response. Additionally, our findings suggest that this modification redirects HIF-2 from its normal transcription factor function towards a role in mRNA fate control, as indicated by mass spectrometry interactome analysis and RNA-immunoprecipitation. Our discoveries highlight a new regulatory mechanism of HIF-2 activity, where S345 phosphorylation impedes HIF-2/HIF-1{beta} heterodimer formation, creating a switch in HIF-2 function. As HIF-2 is the only HIF- isoform with a clinically approved inhibitor, these insights are crucial for advancing therapeutic strategies targeting hypoxia signalling.

molecular biology↗

KDM2B controls HIF levels and activity through its JmjC and CxxC domains

Hypoxia-inducible factors (HIFs) are key regulators of cellular responses to low oxygen (hypoxia), controlling the expression of genes required for survival and adaptation. KDM2B, a chromatin-modifying enzyme, is a direct target of HIF-1, but its precise role in regulating HIF and the hypoxia response remains unclear. Here, we investigated the role of KDM2B in the response to hypoxia in a variety of cell lines. Our analysis reveals that KDM2B depletion regulates HIF activity in a cell type-dependent manner, with KDM2B depletion decreasing HIF activity in U2OS and MDA-MB-231 cells and increasing HIF activity in HeLa cells. We show that KDM2B depletion also reduces HIF-1 protein and RNA expression and reduces HIF-1 binding at hypoxia-response elements of its target genes in U2OS and MDA-MB-231 cells. Conversely, overexpression of KDM2B enhances HIF activity and HIF-1 levels in both U2OS and HEK293 cells. Mechanistically, we find that KDM2B requires its JmjC demethylase and CxxC DNA-binding domains for HIF regulation. Furthermore, we demonstrate that KDM2B is required for RNA Pol II recruitment to the promoter of HIF1A. At the cellular level, KDM2B supports cell proliferation, with its depletion impairing proliferation and reducing cell numbers under hypoxic conditions. Our work highlights a new function of KDM2B as a key regulator of HIF-1 expression, acting through its demethylase and DNA-binding functions. Our data indicate that KDM2B is essential for cellular adaptation to hypoxia, impacting both HIF-dependent gene expression and cell survival, and has important implications for our understanding of HIF regulation.

molecular biology↗

From Sensor Design to Force Maps: A Systematic Evaluation of FRET-based Vinculin Tension Sensors

Mechanical forces transmitted through focal adhesions regulate cell behavior and disease progression, yet remain difficult to quantify at the molecular level. Genetically encoded FRET-based tension probes enable measurements of piconewton-scale forces across specific proteins in living cells, but their quantitative interpretation is highly sensitive to probe design and measurement modality. Here, we systematically compared vinculin tension sensors under identical experimental conditions, evaluating unloaded reference constructs, fluorophore pairs, mechanical sensor modules, and circularly permuted variants. Unloaded controls established a common no-force baseline and validated force-dependent readout. Among the fluorophore pairs tested, the green-red combination Clover-mScarlet-I yielded a higher unloaded FRET efficiency and hence a broader measurable dynamic range. Comparison of six mechanical sensor modules identified the binary-response sensors FL and CC-S2 as the most responsive, showing the largest force-dependent FRET changes and broadest FRET distributions. At the sub-focal adhesion level, CC-S2 reported the steepest proximal-to-distal tension gradient, indicating that vinculin tension increases sharply along peripheral adhesions and exceeds 10 piconewton. Circular permutation experiments revealed that fluorophore orientation has a strong, module-dependent influence on the measured FRET readout. Together, these results establish a comparative framework for interpreting FLIM-based vinculin tension measurements and provide practical design principles for selecting and engineering molecular tension probes.

biophysics↗

A time-calibrated phylogeny of hummingbirds supports stepwise diversification in the Andes

Hummingbirds (Trochilidae) represent the second largest avian family, with [~]356 species occupying diverse habitats across the Neotropical and Nearctic regions. Their extensive diversification includes notable adaptations to extreme environments, with nearly one-third of extant taxa belonging to the predominantly high-altitude Coquettes and Brilliants. Although recent work proposed a monophyletic Andean clade uniting these groups, consistent with rapid radiation during Andean orogeny, we find no support for this relationship. Using 2,949 nuclear loci sampled from 47 species spanning all nine major hummingbird clades, we recover a different evolutionary pattern: a stepwise sequence of diversification in which Brilliants are sister to a broader assemblage comprising Coquettes, the genus Patagona, Emeralds, Mountain Gems, and the recently diverged Bees. By assembling complete mitochondrial genomes, we additionally detect significant discordance between nuclear topologies and those derived from the mitogenome and Z chromosome. Analyses of gene-tree heterogeneity show that incomplete lineage sorting is pervasive across the phylogeny, with particularly strong impacts on branches associated with Andean diversification. Divergence-time estimation further indicates that the major Andean radiation--including Brilliants, Coquettes, Emeralds, Bees, and Mountain Gems--originated around [~]14 Ma, with the three younger clades diversifying [~]12 Ma, coinciding with both the mid-Miocene Andean uplift and the mid-Miocene Climate Transition that increased habitat heterogeneity and likely promoted rapid speciation. To support future phylogenomic efforts, we identify a reduced set of highly informative, independent protein-coding loci and present a near-complete species-level phylogeny constrained by our autosomal backbone. Our findings highlight the importance of integrating loci with distinct inheritance modes to detect and interpret phylogenetic incongruence in rapid radiations.

evolutionary biology↗

3D Cell-Matrix Mechanical Interaction Models for Cancer Invasion and Drug Evaluation

Cancer cells breach the extracellular matrix (ECM) using both protease-driven degradation and force-driven physical remodeling, yet most anti-metastatic drug screens still rely on biochemical assays that overlook cell-matrix mechanical reciprocity. Here, we present a fully synthetic 3D invasion platform based on cellular force-responsive polyisocyanide (PIC) hydrogels that isolates biophysical invasion mechanisms. Cell-generated forces align and densify the PIC fibrous network, reproducing hallmark matrix remodeling seen in the tumor microenvironment. A constitutive model, parameterized by the critical stress for strain stiffening effect, links matrix nonlinear elasticity to pericellular stiffening, long-range mechanotransmission, and intercellular coupling. Using this system, we show that breast cancer cells invade by pulling and pushing the network even when matrix metalloproteinases are inhibited, revealing a physical bypass of protease blockade. Accordingly, broad-spectrum metalloproteinase inhibitors that suppress invasion in Matrigel fail to inhibit invasion here, exposing a limitation of current drug-evaluation pipelines. In co-culture, cancer-associated fibroblasts markedly accelerate invasion by generating aligned fiber tracks through higher contractility, implicating CAF-driven mechanical remodeling as a key route for breaching barriers during metastasis. The platform is thermoresponsive, compatible with standard Transwell formats, enables direct imaging of fiber architecture and invasion fronts, and decouples biophysical from biochemical cues for mechanism-aware, animal-free assessment of anti-metastatic therapies.

cancer biology↗

Label-Free Monitoring of Cancer-associated Fibroblast Activation using NADH Fluorescence Lifetime Imaging

Cancer-associated fibroblasts (CAFs) are key regulators of tumor progression, yet their activation state is commonly assessed using static, endpoint assays that do not allow dynamic analysis in living cells. Although CAF activation is accompanied by pronounced metabolic remodeling, label-free approaches that exploit these changes for real-time monitoring remain limited. Here, we demonstrate that NADH fluorescence lifetime imaging microscopy (FLIM) provides a non-invasive readout of this process. CAFs activated with transforming growth factor beta (TGF-{beta}) exhibit a reproducible shift toward longer NADH fluorescence lifetimes compared to non-activated cells, consistent with changes in the relative contributions of free and protein-bound NADH. By combining live-cell FLIM with -smooth muscle actin staining in the same cells, we directly link metabolic signatures to cellular activation state. We further demonstrate the potential of this approach to dynamically monitor CAF activation in live, migrating cells. Together, these results establish NADH fluorescence lifetime imaging as a label-free metabolic approach for monitoring CAF activation dynamics, complementing conventional marker-based methods and enabling continuous monitoring of tumor-stroma interactions.

biochemistry↗

Quantitative Analysis of Cytoplasmic Viscosity in Colorectal Cancer Cells by Differential Dynamic Microscopy of Genetically Encoded Nanoparticles

The viscosity of the cytoplasm plays a key role in regulating molecular diffusion and cellular mechanics, yet quantifying it in living cells remains technically challenging. Genetically encoded multimeric nanoparticles (GEMs) have emerged as powerful probes for intracellular microrheology; however, current analyses rely on single-particle tracking, which is limited by probe density, imaging noise, and expression variability. Here, we combine GEMs with differential dynamic microscopy (DDM) to enable quantitative, non-invasive, and rapid measurement of intracellular viscosity using standard wide-field fluorescence imaging. DDM extracts particle dynamics from ensemble spatiotemporal intensity fluctuations, yielding reliable diffusion coefficients and viscosity values even in crowded or heterogeneous environments where tracking fails. Validation with fluorescent nanoparticles diffusing in water confirmed that DDM accurately reproduced theoretical viscosities across a wide range of particle sizes and concentrations. Comparison with single-particle tracking (SPT) demonstrated equivalent precision under dilute conditions and superior robustness under crowding. To showcase the potential of this approach, we applied GEM-DDM to colorectal cancer cell lines with different metastatic potentials. Cytoplasmic viscosity correlated with aggressiveness, increasing from 1.9-2.3 cP in poorly metastatic to 3.6-3.7 cP in highly metastatic lines, consistent with greater macromolecular crowding and cytoplasmic reorganization reported in aggressive cells. Together, these results establish GEM-DDM as a fast, reproducible, and accessible platform for intracellular microrheology, providing new opportunities to link the physical state of the cytoplasm to cell function and disease progression. Statement of significancePhysical properties such as cytoplasmic viscosity influence how molecules move and interact within cells, affecting metabolism, signalling, and disease progression. Measuring viscosity in living cells has been technically challenging and often invasive. Here, we introduce GEM-DDM as a quantitative, non-invasive image-based analysis method combining genetically encoded multimeric nanoparticles (GEMs) with differential dynamic microscopy (DDM) to measure intracellular viscosity using standard wide-field microscopy. We validate its accuracy against established single particle tracking (SPT) methods and demonstrate its biological relevance by showing that cytoplasmic viscosity increases with metastatic potential in cancer cells. This approach provides an accessible platform for studying how the physical state of cells influences their function and pathology.

biophysics↗

NRF2 upregulation by CDDO-Me protects AC16 human cardiomyocytes against doxorubicin-induced toxicity.

Doxorubicin (DOX) is an effective anticancer therapeutic but exhibits dose-dependent, potentially life-threatening cardiotoxicity. The specific mechanisms driving this cardiotoxicity are not fully understood but can include the induction of oxidative stress and subsequent cell death mechanism activation. This has prompted the exploration of NRF2, a master co-ordinator of antioxidant and largely cytoprotective pathways, as a potential approach for the alleviation of DOX-induced cardiotoxicity. Here, NRF2 was pharmacologically activated via CDDO-Me (hitherto referred to as CDDO) to reduce the negative consequences on AC16 human cardiomyocyte cell health and functions. NRF2 intracellular dynamics were quantitatively measured using live-cell imaging, demonstrating rapid ([~]10 min) yet sustained ([≥]24 h) induction of NRF2 expression and functional downstream activity. Genetic perturbations of the NRF2-KEAP1 system highlight that CDDO acts specifically through NRF2 to exert AC16 cytoprotection from DOX whilst not promoting human lung and pancreatic cancer cell line viability. Via RNA-seq analysis, we reveal that CDDO dampens DOX-mediated effects on p53 signalling, apoptosis and ferroptosis. This study provides novel insight into NRF2 dynamics in the widely utilised AC16 cells whilst further elucidating the molecular mechanisms contributing to DOX cardiotoxicity and potential NRF2-orchestrated defence. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/675420v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@18c0bb5org.highwire.dtl.DTLVardef@154c707org.highwire.dtl.DTLVardef@d6c127org.highwire.dtl.DTLVardef@122ef0d_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

KLinterSel: Intersection among candidates of different selective sweep detection methods

Detecting signals of natural selection, including selective sweeps, in genomic data often involves applying several methods in parallel. Regions identified by multiple approaches are usually considered strong candidates, as agreement among methods is often taken as supporting evidence. However, the extent to which such overlaps exceed random expectations is rarely evaluated formally. When genomic elements are not independent, coincident candidate sites may arise from the underlying structure of the data rather than from genuine methodological concordance. To address this problem, we introduce two complementary statistical tests designed to evaluate whether the observed overlap among candidate sites detected by different methods exceeds what would be expected by chance. The first is a fast parametric test based on a sequentially conditioned hypergeometric framework that evaluates k-way intersections among candidate sets across genomic windows. The second relies on Monte Carlo simulations and compares the observed inter-method distance profiles with those expected under random association, taking into account the empirical distribution of SNPs along the genome. By capturing different aspects of concordance, these approaches allow agreement among methods to be assessed across multiple spatial scales. Both tests are implemented in the program KLinterSel, which also identifies clusters of candidate sites detected by different selection-detection methods within a user-defined distance threshold. We illustrate its application using candidate loci associated with resistance of the common cockle (Cerastoderma edule) to the parasite Marteilia cochillia. The software is written in Python and is available on GitHub together with documentation and precompiled executables for major operating systems.

genomics↗

Exploring Hypoxia-Related Genes as Prognostic Indicators in Lung Adenocarcinoma

BackgroundLung adenocarcinoma (LUAD) is a leading cause of cancer-related mortality, with hypoxia contributing to tumor progression and treatment resistance. Identifying hypoxia-related biomarkers could enhance prognosis and therapeutic strategies for LUAD. MethodsThis study aimed to identify hypoxia-related differentially expressed genes (HRDEGs) in lung adenocarcinoma (LUAD) through differential expression analysis. Functional analysis and protein-protein interaction (PPI) network construction were performed to explore the biological roles and interactions of these genes. Kaplan-Meier survival analysis, univariate Cox regression, and Lasso regression were used to identify key genes associated with survival. Multivariate Cox regression was then conducted to assess independent prognostic factors. ResultsThis analysis revealed 283 upregulated HRDEGs and 322 downregulated HRDEGs in LUAD. Functional enrichment analysis indicated that the upregulated genes were primarily involved in cancer-related and cellular signaling pathways, while downregulated genes were associated with immunity-related pathways. We further identified 201 common upregulated hub genes (including MMP9, CDH1, HSP90AB1, SOX2, CDKN2A, SPP1, EZH2) and 224 common downregulated hub genes (such as IL6, TNF, IL1B, JUN, CCL2, TLR4, FOS, PTGS2). Kaplan-Meier survival analysis, univariate Cox regression, and Lasso regression led to the identification of 17 key genes (ADRB2, ALDH2, CAT, CCNE1, MAP3K8, DSG2, EIF6, ABCB1, PIK3R1, RAD51, SFTPD, SOD3, CLEC3B, ADAM12, EXO1, FBLN5, and IGF2BP3) associated with patient survival. Finally, multivariate Cox regression analysis identified DSG2, EIF6, and EXO1 as independent prognostic factors for LUAD, highlighting their potential as biomarkers for prognosis and therapeutic targets in lung cancer. ConclusionIn conclusion, DSG2, EIF6, and EXO1 were identified as key hypoxia-related genes in lung adenocarcinoma. These genes were found to be independent prognostic factors, highlighting their potential as biomarkers for predicting patient survival and guiding future therapeutic approaches. Authors summaryThis study investigates the role of hypoxia-related genes in lung adenocarcinoma (LUAD), a major cause of cancer mortality. By analyzing gene expression data, this study identified 283 upregulated and 322 downregulated hypoxia-related differentially expressed genes (HRDEGs). Functional enrichment analysis revealed that the upregulated genes are largely involved in cancer progression and cell signaling, while the downregulated ones are linked to immune responses. A set of key hub genes was identified through protein-protein interaction analysis. Using survival analysis tool, 17 genes significantly associated with patient outcomes in two different patient cohorts. Among these, confirmed three genes--DSG2, EIF6, and EXO1--were confirmed as independent prognostic markers. These findings suggest that these genes may serve as valuable biomarkers for predicting survival and developing targeted therapies in LUAD, offering new avenues for improving patient management in hypoxia-driven tumors.

bioinformatics↗

PHD1-dependent hydroxylation of RepoMan (CDCA2) on P604 modulates the control of mitotic progression

Prolyl-hydroxylases (PHDs) are oxygen sensing enzymes that mediate the hydroxylation of proline residues. In mammals, three PHD isoforms (PHD1-3) are responsible for proline hydroxylation of Hypoxia Inducible Factor (HIF) alpha, a key regulator of the hypoxia response. In the accompanying paper (Jiang et. al., 2025) we report development of a mass spectrometry-based method to reliably identify proline hydroxylation (OH-Pro) sites on proteins and use this to identify a PHD-dependent OH-Pro modification at Pro604 on the protein RepoMan (CDCA2), a regulatory subunit for protein phosphatase PP1{gamma}, with important roles in mitotic progression and cell viability. Here, we investigate the functional significance of hydroxylation of RepoMan at P604. During M phase, the PP1-RepoMan complex dephosphorylates Thr3 of Histone H3 (H3T3) on chromosomes arms to ensure the correct localisation of the chromosomal passenger complex (CPC) at centromeres. We show that siRNA depletion of PHD1, but not PHD2, increases H3T3 phosphorylation in prometaphase-arrested cells. In cells depleted of endogenous RepoMan, exogenous expression of wild type RepoMan, but not a RepoMan P604A mutant, restored normal H3T3 phosphorylation localisation in prometaphase arrested cells. RepoMan P604 is located proximal to the Short Linear Motifs (SLiMs) that function as binding sites for the serine/threonine Protein Phosphatase 2A (PP2A). The interaction of RepoMan and PP2A-B56{gamma} is reduced in cells expressing RepoMan P604A. Moreover, analyses in both fixed and live cells released from a prometaphase arrest, show that expression of the RepoMan P604A mutant delays completion of mitosis, results in defects in chromosome alignment and segregation and increases levels of cell death. These data support a role for PHD1-mediated prolyl hydroxylation in controlling progression through mitosis, acting, at least in part, via hydroxylation of RepoMan at P604 regulating the interaction of RepoMan with PP2A during chromosome alignment and thereby controlling the levels of Histone H3 phosphorylation at Thr3.

cell biology↗

Beyond One-Size-Fits-All: Tumor Biology Influences Nanoparticle Behaviour in Cancer Models

Nanoparticles (NPs) are a promising tool for cancer therapy, yet few have successfully reached clinical application. Current nanomedicine development pipelines are focused on optimizing physical properties of NPs, overlooking the impact of tumor biology on their behavior. Here, we show that the same NPs exhibit distinct accumulation and penetration patterns in 3D spheroids derived from four tumor models (representative of lung, colon, breast, and cervical cancer). We uncover an inverse relationship between NP uptake and penetration: tumors with slower internalization show deeper NP diffusion. Proteomic analysis revealed that tumor-specific expression of endocytic and extracellular matrix proteins underlies this variability. Our findings challenge the prevailing one-size-fits-all approach and highlight the need to integrate tumor biology into NP design. Tailoring NPs to the unique cellular and extracellular features of each tumor type will be critical for developing more effective and clinically relevant nanotherapies.

cell biology↗

Cellular Responses to Photothermal Therapy: Heat-Induced ERK Signaling and Intercellular Communication in Solid Tumors

Nanoparticle-mediated photothermal therapy (PTT) shows promise as a standalone cancer treatment but faces clinical challenges due to inconsistent efficacy. Its translation is further hindered by a limited understanding of plasmon-induced heat effects, such as stress responses and intercellular signaling. Here, we investigate how plasmon-induced local heating affects cellular behavior and fate within tumor spheroids by focusing on the activity of the extracellular signal-regulated kinase (ERK). Spheroids were prepared from HeLa cells that express a FRET-based ERK sensor, and ERK activity changes under photothermal stimuli were tracked using a deep-learning program, 3DeeCellTracker. Gold nanostars were used as highly efficient photothermal transducers. Our results revealed significant alterations in ERK signaling patterns upon photothermal stimulation compared to spontaneous ERK activity in untreated spheroids, including changes in the activation frequency, timing, and duration. Notably, photothermal-induced ERK activity propagated across neighboring cells within the spheroid, suggesting intercellular communication. Furthermore, analysis of cell death and division further demonstrated that laser power modulates cellular fate during photothermal therapy. This study provides insights for predicting the therapeutic effects of PPT and guides the rational design of next-generation photothermal strategies. Additionally, our approach demonstrates the potential of FRET-based biosensors and deep-learning tools as powerful methods to study the effects of various therapeutic stimuli on solid tumors at the single-cell level.

cancer biology↗