Objectives Understanding the molecular changes in the preclinical synovium is crucial for identifying factors that drive arthritis development. Persistent DNA damage in tissues is known to drive a senescent microenvironment, genomic instability and ultimately chronic inflammation. Here, we determined cellular DNA damage and repair capacity within synovial tissue from rheumatoid arthritis (RA) patients and individuals at risk of developing RA.Methods We investigated the presence of senescence-associated DNA damage in synovial biopsies and synovial fibroblasts obtained during different phases of RA. Histone 2A is phosphorylated (γH2AX) at the site of a double-stranded DNA break where DNA repair proteins are recruited and is therefore a proxy measurement for DNA damage. In this study, we employed immunofluorescence staining for γH2AX on synovial tissue sections and cultured synovial fibroblasts alongside quantitative PCR for a panel of DNA repair proteins.Results We demonstrated the presence of DNA damage in both synovial fibroblasts and T cells during the preclinical, RA-risk phase of disease. Furthermore, cultured synovial fibroblasts from RA-risk individuals and RA patients exhibited increased DNA damage and a reduced capacity for DNA repair compared with synovial fibroblasts from control individuals. Finally, treatment with senolytic drugs partially restored the DNA damage repair capacity in RA and RA-risk synovial fibroblasts in vitro.Conclusions Our findings reveal persistent DNA damage in the preclinical phase of RA in both synovial tissue and fibroblasts, suggesting a role in disease progression. The partial restoration of DNA repair in synovial fibroblasts by senolytic treatment highlights its potential therapeutic target for preventative therapy in RA-risk individuals.

Cell competition is an evolutionarily conserved quality control mechanism that eliminates less-fit cells to ensure optimal tissue integrity during development, homeostasis, and regeneration. Beyond these physiological roles, recent evidence implicates a role for cell competition in disease, particularly in cancer, where it can function by either suppressing or promoting malignant progression. In this review, we provide an overview of the different molecular mechanisms that drive cell competition and their impact on cancer development and progression. We will evaluate the current state-of-the-art in vitro experimental systems that can be employed to study these processes. Ranging from classical 2D co-culture systems to advanced organoid and organ-on-chip platforms, these model systems collectively enhance our understanding of the complex cellular interactions that underlie the competitive differences between cells. By integrating insights from diverse model systems, we highlight how cell competition shapes tumor dynamics and discuss how this knowledge could inspire novel therapeutic strategies to prevent or control tumor growth.

Background: Efficacy of current treatment options for cervical cancer require improvement. Previous in vitro studies have shown the enhancing effects of the addition of PARP1-inhibitors to chemoradiotherapy and thermoradiotherapy. The aim of our present study was to test efficacy of different combinations of treatment modalities radiotherapy, cisplatin, hyperthermia and PARP1-inhibitors using in vitro tumor models, ex vivo treated patient samples and in vivo tumor models.Materials and Methods: In vitro clonogenic survival curves (0-6 Gy) show that PARP1-i (4-5 M Olaparib) enhances both chemoradiotherapy (0.3-0.5 mu M cisplatin) and thermoradiotherapy (42 degrees C for 1 h) in SiHa, CaSki and HeLa cells. A cervical cancer mouse model and freshly obtained in-house developed patient-derived organoids were used to examine the effects of different treatment combinations. For the in vivo study, human cervical cancer (SiHa) cells were injected in the right hind leg of athymic nude mice. In vivo mouse experiments show that PARP1-i enhances thermoradiotherapy or chemoradiotherapy by reduction of tumor volumes. Five cycles of treatment were applied with the following doses per cycle: irradiation 3 Gy, hyperthermia 1 h at 42 degrees C, cisplatin at 2 mg/kg, and twice PARP1-i at 50 mg/kg.Results: Quadruple treatment, combining radiotherapy, hyperthermia, cisplatin and PARP1-i, was very effective but also lead to severe side effects causing severe weight loss and death. In contrast, thermoradiotherapy or chemoradiotherapy with addition of PARP1-i, were effective without serious side effects.Conclusion: The triple combinations are promising options for potentially more effective treatment of locally advanced cervical cancer without more toxicity.

Clonal dispersal, resulting from the intermingling of tumor cell subpopulations, is thought to be a key driver of tumor heterogeneity. Despite advances in spatial modeling of cancer biology, quantification of clonal dispersal has been challenging. This study introduces a straightforward method, relying on fluorescent cell barcoding, to quantify clonal dispersal in various in vitro and in vivo models of colorectal cancer (CRC). Our approach allows for precise localization of clones and uncovering the degree of clonal mixing across different CRC models. Our findings suggest that clonal dispersal is correlated with the expression of genes involved in epithelial-mesenchymal transition and CMS4-related signaling pathways. We further identify a dispersal gene signature, associated with intratumor heterogeneity, which is a robust clinical predictor of poor prognosis and recurrence in CRC, highlighting its potential as a prognostic marker and a putative direction for therapeutic targeting.

INTRODUCTION:This preclinical study evaluated the effects of combining hypofractionated radiation (HFRT), either as X-ray photons or protons, with hyperthermia on tumor response and normal tissue damage in mice. METHODS:The tumors were C3H mammary carcinomas implanted in the right rear foot of male CDF1 mice, while non-tumor-bearing mice were used to assess normal foot skin. HFRT was delivered in three fractions (5, 10, or 15 Gy) at 3 to 4-day intervals. Hyperthermia (40.5-42.5 °C) was applied once for 60 min, either 30, 90, or 180 min after the final radiation dose. Endpoints included tumor growth delay and moist skin desquamation. Mechanistic studies assessed DNA damage (γ-H2AX foci) 24 h after 3 × 10 Gy, with or without hyperthermia (42.5 °C for 1 h, administered 30 min post-RT), and tumor hypoxia (pimonidazole staining) measured 1 h after the last radiation fraction. RESULTS:Animals responded similarly to X-ray photons and protons in the tumor and skin. Hyperthermia enhanced the response to X-ray photons in both tissues, with temperature and time-interval dependency, showing the greatest effects at higher temperatures and shorter intervals. Protons combined with hyperthermia showed similar results, although with less decay in time-interval effects at 42.5 °C. DNA damage assessments revealed no significant difference between radiation types, but a significant enhancement was seen when tumors were heated at 42.5 °C. Tumor hypoxia was reduced after 3 × 10 Gy irradiation with either radiation type. CONCLUSIONS:Combining HFRT with hyperthermia yielded effects comparable to single-dose studies for both tumors and normal tissues. These responses were similar for both X-rays and protons.

Introduction Cell repair dynamics are crucial in optimizing anti-cancer therapies. Various assays (eg, comet assay and γ-H2AX) assess post-radiation repair kinetics, but interpreting such data is challenging and model-based data analyses are required. However, ambiguities in parameter calibration remain an unsolved challenge. To address this, we propose combining survival dose-rate effects with computer simulations to gain knowledge about repair kinetics. Methods After a literature review, theoretical discriminators based on common fractionation/dose-rate-related effects were defined to discard unrealistic model dynamics. The Multi-Hit Repair (MHR) model was calibrated with canine osteosarcoma Abrams cell line data to study the discriminators’ efficacy in scenarios with limited survival data. Additionally, survival dose-rate-dependent data from the human SiHa cervical cancer cell line were used to illustrate the survival behavior at diverse dose-rates and the capability of the MHR to model these data. Results SiHa data confirmed the validity of the proposed discriminators. The discriminators filtered 99% of parameter sets, improving the calibration of Abrams cells data. Furthermore, results from both cell lines may hint universal aspects of cellular repair. Conclusions Dose-rate theoretical discrimination criteria are an effective method to understand repair kinetics and improve radiobiological model calibration. Moreover, this methodology may be used to analyze diverse biological data using dynamic models in-silico . Keywords repair kinetics , dose-rate , radiobiological models

In the rapidly evolving field of bioimaging, the integration and orchestration of Findable, Accessible, Interoperable, and Reusable (FAIR) image analysis workflows remains a challenge. We introduce BIOMERO, a bridge connecting OMERO, a renowned bioimaging data management platform, FAIR workflows and high-performance computing (HPC) environments. BIOMERO, featuring our open-source Python library "OMERO Slurm Client", facilitates seamless execution of FAIR workflows, particularly for large datasets from High Content or High Throughput Screening. BIOMERO empowers researchers by eliminating the need for specialized knowledge, enabling scalable image processing directly from OMERO. BIOMERO notably supports the sharing and utilization of FAIR workflows between OMERO, Cytomine/BIAFLOWS, and other bioimaging communities. BIOMERO will promote the widespread adoption of FAIR workflows, emphasizing reusability, across the realm of bioimaging research. Its user-friendly interface will empower users, including those without technical expertise, to seamlessly apply these workflows to their datasets, democratizing the utilization of AI by the broader research community.

Introduction Cell repair dynamics are crucial in optimizing anti-cancer therapies. Various assays (eg, comet assay and γ-H2AX) assess post-radiation repair kinetics, but interpreting such data is challenging and model-based data analyses are required. However, ambiguities in parameter calibration remain an unsolved challenge. To address this, we propose combining survival dose-rate effects with computer simulations to gain knowledge about repair kinetics. Methods After a literature review, theoretical discriminators based on common fractionation/dose-rate-related effects were defined to discard unrealistic model dynamics. The Multi-Hit Repair (MHR) model was calibrated with canine osteosarcoma Abrams cell line data to study the discriminators’ efficacy in scenarios with limited survival data. Additionally, survival dose-rate-dependent data from the human SiHa cervical cancer cell line were used to illustrate the survival behavior at diverse dose-rates and the capability of the MHR to model these data. Results SiHa data confirmed the validity of the proposed discriminators. The discriminators filtered 99% of parameter sets, improving the calibration of Abrams cells data. Furthermore, results from both cell lines may hint universal aspects of cellular repair. Conclusions Dose-rate theoretical discrimination criteria are an effective method to understand repair kinetics and improve radiobiological model calibration. Moreover, this methodology may be used to analyze diverse biological data using dynamic models in-silico.

Peritoneal metastases (PMs) from colorectal cancer (CRC) respond poorly to treatment and are associated with unfavorable prognosis. For example, the addition of hyperthermic intraperitoneal chemotherapy (HIPEC) to cytoreductive surgery in resectable patients shows limited benefit, and novel treatments are urgently needed. The majority of CRC-PMs represent the CMS4 molecular subtype of CRC, and here we queried the vulnerabilities of this subtype in pharmacogenomic databases to identify novel therapies. This reveals the copper ionophore elesclomol (ES) as highly effective against CRC-PMs. ES exhibits rapid cytotoxicity against CMS4 cells by targeting mitochondria. We find that a markedly reduced mitochondrial content in CMS4 cells explains their vulnerability to ES. ES demonstrates efficacy in preclinical models of PMs, including CRC-PMs and ovarian cancer organoids, mouse models, and a HIPEC rat model of PMs. The above proposes ES as a promising candidate for the local treatment of CRC-PMs, with broader implications for other PM-prone cancers.

DNA double-strand breaks initiate the DNA damage response (DDR), leading to the accumulation of repair proteins at break sites and the formation of the-so-called foci. Various microscopy methods, such as wide-field, confocal, electron, and super-resolution microscopy, have been used to study these structures. However, the impact of different DNA-damaging agents on their (nano)structure remains unclear. Utilising GSDIM super-resolution microscopy, here we investigated the distribution of fluorescently tagged DDR proteins (53BP1, RNF168, MDC1) and γH2AX in U2OS cells treated with γ-irradiation, etoposide, cisplatin, or hydroxyurea. Our results revealed that both foci structure and their nanoscale ultrastructure, including foci size, nanocluster characteristics, fluorophore density and localisation, can be significantly altered by different inducing agents, even ones with similar mechanisms. Furthermore, distinct behaviours of DDR proteins were observed under the same treatment. These findings have implications for cancer treatment strategies involving these agents and provide insights into the nanoscale organisation of the DDR.

In the rapidly evolving field of bioimaging, the integration and orchestration of findable, accessible, interoperable, and reusable (FAIR) image analysis workflows remains a challenge. We introduce BIOMERO (bioimage analysis in OMERO), a bridge connecting OMERO, a renowned bioimaging data management platform; FAIR workflows; and high-performance computing (HPC) environments. BIOMERO facilitates seamless execution of FAIR workflows, particularly for large datasets from high-content or high-throughput screening. BIOMERO empowers researchers by eliminating the need for specialized knowledge, enabling scalable image processing directly from OMERO. BIOMERO notably supports the sharing and utilization of FAIR workflows between OMERO, Cytomine/BIAFLOWS, and other bioimaging communities. BIOMERO will promote the widespread adoption of FAIR workflows, emphasizing reusability, across the realm of bioimaging research. Its user-friendly interface will empower users, including those without technical expertise, to seamlessly apply these workflows to their datasets, democratizing the utilization of AI by the broader research community.

Temporary elevation of tumor temperature, also known as hyperthermia, is a safe and well-tolerated treatment modality. The efficacy of hyperthermia can be improved by efficient thermosensitizers, and various candidate drugs, including inhibitors of the heat stress response, have been explored in vitro and in animal models, but clinically relevant thermosensitizers are lacking. Here, we employ unbiased in silico approaches to uncover new mechanisms and compounds that could be leveraged to increase the thermosensitivity of cancer cells. We then focus on elesclomol, a well-performing compound, which amplifies cell killing by hyperthermia by 5- to 20-fold in cell lines and outperforms clinically applied chemotherapy when combined with hyperthermia in vitro. Surprisingly, our findings suggest that the thermosensitizing effects of elesclomol are independent of its previously reported modes of action but depend on copper shuttling. Importantly, we show that, like elesclomol, multiple other copper shuttlers can thermosensitize, suggesting that disturbing copper homeostasis could be a general strategy for improving the efficacy of hyperthermia.

Hyperthermia (HT) is an accepted treatment for recurrent breast cancer which locally heats the tumor to 39–44 °C, and it is a very potent sensitizer for radiotherapy (RT) and chemotherapy. However, currently little is known about how HT with a distinct temperature, and particularly, how the sequence of HT and RT changes the immune phenotype of breast cancer cells. Therefore, human MDA-MB-231 and MCF-7 breast cancer cells were treated with HT of different temperatures (39, 41 and 44 °C), alone and in combination with RT (2 × 5 Gy) in different sequences, with either RT or HT first, followed by the other. Tumor cell death forms and the expression of immune checkpoint molecules (ICMs) were analyzed by multicolor flow cytometry. Human monocyte-derived dendritic cells (moDCs) were differentiated and co-cultured with the treated cancer cells. In both cell lines, RT was the main stressor for cell death induction, with apoptosis being the prominent cell death form in MCF-7 cells and both apoptosis and necrosis in MDA-MB-231 cells. Here, the sequence of the combined treatments, either RT or HT, did not have a significant impact on the final outcome. The expression of all of the three examined immune suppressive ICMs, namely PD-L1, PD-L2 and HVEM, was significantly increased on MCF-7 cells 120 h after the treatment of RT with HT of any temperature. Of special interest for MDA-MB-231 cells is that only combinations of RT with HT of both 41 and 44 °C induced a significantly increased expression of PD-L2 at all examined time points (24, 48, 72, and 120 h). Generally, high dynamics of ICM expression can be observed after combined RT and HT treatments. There was no significant difference between the different sequences of treatments (either HT + RT or RT + HT) in case of the upregulation of ICMs. Furthermore, the co-culture of moDCs with tumor cells of any treatment had no impact on the expression of activation markers. We conclude that the sequence of HT and RT does not strongly affect the immune phenotype of breast cancer cells. However, when HT is combined with RT, it results in an increased expression of distinct immune suppressive ICMs that should be considered by including immune checkpoint inhibitors in multimodal tumor treatments with RT and HT. Further, combined RT and HT affects the immune system in the effector phase rather than in the priming phase.

Clonal proliferation dynamics within a tumor channels the course of tumor growth, drug response and activity. A high-throughput image screening technique is required to analyze and quantify the spatiotemporal variations in cell proliferation and influence of chemotherapy on clonal colonies. We present two protocols for generating spatial, Lentiviral Gene Ontology (LeGO) fluorescent tag based, mono- and co-culture systems with provisions for spatio-temporal tracking of clonal growth at the nucleus- and cytoplasm-level. The cultured cells are subjected to either drug treatment or co-cultured with fibroblasts and analyzed with a novel image processing framework. This framework enables alignment of cell positions based on motion capture techniques, tracking through time and investigation of drug actions or co-culturing on individual cell colonies. Finally, utilizing this framework, we develop agent-based models to simulate and predict the effects of the microenvironment and clonal density on cell proliferation. The model and experimental findings suggest growth stimulating effects of local clonal density irrespective of overall cell confluency.

Clonal growth and competition underlie processes of key relevance in etiology, progression and therapy response across all cancers. Here, we demonstrate a novel experimental approach, based on multi-color, fluorescent tagging of cell nuclei, in combination with picoliter droplet deposition, to study the clonal dynamics in two- and three-dimensional cell cultures. The method allows for the simultaneous visualization and analysis of multiple clones in individual multi-clonal colonies, providing a powerful tool for studying clonal dynamics and identifying clonal populations with distinct characteristics. Results of our experiments validate the utility of the method in studying clonal dynamics in vitro , and reveal differences in key aspects of clonal behavior of different cancer cell lines in monoculture conditions, as well as in co-cultures with stromal fibroblasts.

Background Cellular senescence is a state of proliferation arrest of cells occurring and cleared during normal aging. However, the persistence and accumulation of senescent cells has been implicated in the pathogenesis of age-related diseases like rheumatoid arthritis (RA). Aging is an important risk factor of RA, a chronic autoimmune disease in which loss of immune tolerance and systemic autoimmunity precedes clinical onset of disease. Lymph node stromal cells (LNSCs) are important regulators of peripheral tolerance. Accordingly, accumulating senescent LNSCs may potentially lead to defective peripheral tolerance and the development of systemic autoimmune disease. Objectives In this study we investigated the senescence phenotype of LNSCs during health, systemic autoimmunity and RA. Additionally, we examined whether dasatinib treatment could restore their cellular phenotype and function. Methods LNSCs were isolated and cultured from inguinal lymph node needle biopsies from autoantibody positive individuals with arthralgia and therefore at risk of developing RA (RA-risk individuals), RA patients and seronegative healthy volunteers. The senescent phenotype and the effect of dasatinib treatment were assessed using quantitative PCR, flow cytometry, microscopy and live-cell analysis. Results Cell size, granularity and autofluorescence were significantly higher in RA LNSCs compared with control LNSCs. Stainings indicate more senescence associated β-galactosidase activity, more lipofuscin granules and increased DNA damage in RA-risk and RA LNSCs compared with control LNSCs. Moreover, we found altered gene expression levels of senescence associated genes in LNSCs from RA patients. Functional experiments showed no difference in proliferation and migration capacity between donor groups. Strikingly, the capacity to repair irradiation induced DNA damage was significantly lower in RA-risk and RA LNSCs compared with control LNSCs. Treating LNSCs with dasatinib significantly improved cell size and DNA repair capacity of cultured LNSCs. Conclusion We observed premature aging of lymphoid stroma in RA patients and to lesser extent already in individuals at risk of developing RA, which could partly be restored by dasatinib treatment. Premature aging of LNSCs may negatively impact the local niche by inducing inflammation and senescence in nearby cells. However, consequences of prematurely aged lymphoid stroma remain inconclusive providing a rationale for investigating the effect on immune cell responses. Acknowledgements We thank our study subjects for participating in the study, the AMC radiology department for lymph node tissue sampling and the rheumatology lab for sample processing. The research leading to these results was funded by an AMC fellowship (to L.G.M.v.B.), the Dutch Arthritis Foundation LLP-30 and the Dutch Organization for Health Research and Development (ZonMw) VIDI n° 91718371 (to L.G.M.v.B). Disclosure of Interests None Declared.

Objective Cellular senescence is a state of proliferation arrest of cells occurring during aging. The persistence and accumulation of senescent cells has been implicated in the pathogenesis of age-related diseases like rheumatoid arthritis (RA). RA is a chronic autoimmune disease in which loss of immune tolerance and systemic autoimmunity precedes clinical onset of disease. Lymph node stromal cells (LNSCs) are important regulators of immune tolerance. Accordingly, accumulating senescent LNSCs may potentially lead to defective immune tolerance and the development of systemic autoimmune disease.Methods Human LNSCs were isolated and cultured from inguinal lymph node needle biopsies from individuals at risk of developing RA (RA-risk individuals), RA patients and seronegative healthy volunteers. Senescence hallmarks and the effect of dasatinib treatment were assessed using quantitative PCR, flow cytometry, microscopy and live-cell imaging.Results Cell size, granularity and autofluorescence were significantly higher in RA LNSCs compared with control LNSCs. Stainings indicate more senescence associated β-galactosidase activity, more lipofuscin positive granules and increased DNA damage in RA-risk and RA LNSCs compared with control LNSCs. Moreover, we found altered gene expression levels of senescence associated genes in LNSCs from RA patients. Strikingly, the capacity to repair irradiation induced DNA damage was significantly lower in RA-risk and RA LNSCs compared with control LNSCs. Treating LNSCs with dasatinib significantly improved cell size and DNA repair capacity of cultured LNSCs.Conclusion We observed multiple senescent hallmarks in RA LNSCs and to lesser extent already in RA-risk LNSCs, which could partly be restored by dasatinib treatment.What is already known on this topic? What does this study add? How might this study impact on clinical practice or future developments? ### Competing Interest StatementThe authors have declared no competing interest.* RA : rheumatoid arthritis RF : rheumatoid factor ACPA : anti-citrullinated protein antibodies RA-risk : individuals who are positive for RF or/and ACPA and at risk of developing RA LNSC : Lymph node stromal cell

Hyperthermia is clinically applied cancer treatment in conjunction with radio- and/or chemotherapy, in which the tumor volume is exposed to supraphysiological temperatures. Since cells can effectively counteract the effects of hyperthermia by protective measures that are commonly known as the heat stress response, the identification of cellular processes that are essential for surviving hyperthermia could lead to novel treatment strategies that improve its therapeutic effects. Here, we apply a meta-analytic approach to 18 datasets that capture hyperthermia-induced transcriptome alterations in nine different human cancer cell lines. We find, in line with previous reports, that hyperthermia affects multiple processes, including protein folding, cell cycle, mitosis, and cell death, and additionally uncover expression changes of genes involved in KRAS signaling, inflammatory responses, TNF-a signaling and epithelial-to-mesenchymal transition (EMT). Interestingly, however, we also find a considerable inter-study variability, and an apparent absence of a ‘universal’ heat stress response signature, which is likely caused by the differences in experimental conditions. Our results suggest that gene expression alterations after heat stress are driven, to a large extent, by the experimental context, and call for a more extensive, controlled study that examines the effects of key experimental parameters on global gene expression patterns.

The Clonogenic Survival Assay (CSA) is a fundamental tool employed to assess cell survival and proliferative potential in cancer research. Despite its importance, CSA faces limitations, primarily its time- and labor-intensive nature and its binary output. To overcome these limitations and enhance CSA's utility, several approaches have been developed, focusing on increasing the throughput. However, achieving both high-content and high-throughput analyses simultaneously has remained a challenge. In this paper, we introduce LeGO-CSA, an extension of the classical CSA that employs the imaging of cell nuclei barcoded with fluorescent lentiviral gene ontology markers, enabling both high-content and high-throughput analysis. To validate our approach, we contrasted it with results from a classical assay and conducted a proof-of-concept screen of small-molecule inhibitors targeting various pathways relevant to cancer treatment. Notably, our results indicate that the classical CSA may underestimate clonogenicity and unveil intriguing aspects of clonal cell growth. We demonstrate the potential of LeGO-CSA to offer a robust approach for assessing cell survival and proliferation with enhanced precision and throughput, with promising implications for accelerating drug discovery and contributing to a more comprehensive understanding of cellular behavior in cancer.