Saul, Dominik

Abstract Senescent cells accumulate with age and contribute to tissue dysfunction, yet their identification in tissues is challenging due to low abundance, heterogeneous phenotypes, and the lack of specific markers. Senescence-associated features span multiple subcellular compartments, including nuclear DNA damage foci, cytosolic protein changes, and perinuclear alterations, each requiring tailored detection strategies. To overcome these challenges, we developed SenoQuant ( https://github.com/HaamsRee/senoquant ), a versatile software designed for comprehensive, accurate, and unbiased spatial quantification and prediction of senescence markers across diverse tissue contexts. Utilizing AI models, SenoQuant enables precise nuclear and cytoplasmic segmentation and detection of senescence markers across low- and high-plex imaging modalities, applicable to cultured cells and tissue sections from mice and humans. The platform also supports custom AI models; for example, we built SenCeption, a proof-of-concept predictor of single-cell p21 status from DAPI-stained nuclei in human skin. Available as a free napari plugin, SenoQuant is widely accessible to researchers. By providing a unified approach to senescence analysis and prediction, SenoQuant opens new opportunities for exploring the complex biology of senescence and its impacts on aging and disease.

Abstract Transcriptional condensates (TCs) are dynamic, membrane-less assemblies of proteins and nucleic acids that form at specific genomic loci to control gene expression. The primary drivers of TC formation and function are long stretches of polypeptide chains that lack well-defined tertiary structure, known as the intrinsically disordered regions (IDRs) of Transcription Factors (TFs). However, the role of well-structured domains such as the DNA-binding domain (DBD) in condensate formation and downstream regulation remains poorly understood. Here, we investigated whether the DBD of the Progesterone Receptor (PR), a model TF regulated by hormone binding, contributes to the formation of PR TCs. By combining Single Particle Tracking (SPT) with deep-learning-based single-trajectory analysis, we demonstrated that both the IDR and the DBD are required for the formation of PR condensates. Furthermore, transcriptomic analysis showed that mutations of either of the two domains result in the expression of a distinct set of genes, with functional assays corroborating these findings and linking domain-specific transcription to differential effects on cell proliferation and migration. Together, our results show that domains beyond IDRs also play a role in TC formation and function and uncover domain-specific regulation of transcriptional and oncogenic programs.

Key Points This study reveals the temporal development and progression of senescence in an arteriovenous fistula of uremic mice. Senescent genes including p21 increased 7 days after arteriovenous fistula placement, and p16 and phosphorylated p53 cells accumulate between days 14 and 28. Transcriptomic analyses confirm established genes in arteriovenous fistula failure and suggest a collection of novel genes of interest. Background Hemodialysis therapy for ESKD requires suitable vascular access, most commonly the arteriovenous fistula (AVF). Forty percent of AVFs fail within 1 year, leading to morbidity and care costs. Failure mechanisms remain unclear, and current therapies are inadequate. Cellular senescence may be critical in AVF failure, and ESKD itself may accelerate senescence and subsequent vascular dysfunction. Senescence follows AVF placement in rodents with normal kidney function, but the temporal and spatial features in uremic conditions are unknown. This study aimed to characterize AVF changes in uremic mice over time and versus control vessels. Methods Six- to eight-week-old male C57BL6/J mice underwent five/six nephrectomy. Twenty-eight days later, an AVF was created by cuff anastomosis (right carotid artery to the right jugular vein). Transcriptomic analysis was performed 7 days post-AVF, and further samples were collected at 14 and 28 days post-AVF creation for histologic assessment. Results AVF outflow vein morphometry showed reduced neointimal cell density. Whole transcriptomic analysis of outflow versus control veins at 7 days post-AVF placement revealed 1187 upregulated and 3256 downregulated genes. Differentially expressed genes were significantly enriched in two established senescence-related gene sets, SenMayo (a curated panel of approximately 125 genes validated across species to capture senescence and associated proteins) and SenSig (a broader panel assessed to represent fibrotic and stress-induced cell response). Histologically, senescence markers p16, p21, and phospho53 increased between days 14 and 28. Genes common to our dataset, SenMayo, and SenSig were validated with quantitative reverse transcription PCR. Conclusions These data support established markers of AVF failure, such as matrix-metalloproteinases and monocyte chemokines, and identify potential novel modulators of AVF survival that may inform senolytic strategies to improve patency. In summary, this study reveals for the first time the chronologic progression of vascular senescence in the AVF of uremic mice.

ABSTRACT Osteoporosis is a chronic disease mainly prevalent in older people. A hip fracture, its most devastating complication, is associated with a one in five chance of mortality in the first year. This review discusses emerging risk factors for bone fragility including diabetes, sarcopenia, and bariatric surgery. Recency of fracture represents an imminent risk that deserves prompt recognition. The new FRAXplus calculator accounts for additional risk factors to refine existing risk stratification. Advances in imaging techniques such as trabecular bone score and radiofrequency echographic multi-spectrometry may have potential roles in specific populations. Treatment of osteoporosis requires a multifaceted approach. Non-drug interventions include fall prevention and resistance exercises, supplementation with calcium, vitamin D and possibly vitamin K, and effective bridging of care gaps with fracture liaison services. An overview of drug therapy is provided, drawing attention to the importance of sequential therapy starting with potent anabolic agents for the patients at the highest risk, as opposed to a traditional step-up approach. An individualized, goal directed care plan is necessary for a treat-to-target approach, with total hip bone mineral density being the best specific target. Future research in cellular senescence points to the role of senolytics and senomorphics to alleviate osteoporosis, among other age related conditions.

Abstract NF-κB signaling can be subdivided into canonical and noncanonical pathways, culminating in the transcriptional activity of RELA and RELB, respectively. However, the upstream signals that activate these transcription factors and their specific regulatory roles in pancreatic ductal adenocarcinoma (PDAC) remain incompletely understood. Here, we demonstrate that TNFα is the primary activator of canonical NF-κB signaling via RELA, while TWEAK engages noncanonical signaling through RELB in PDAC. Using transcriptome-wide gene expression, genome-wide occupancy profiling, and epigenome mapping, we delineate distinct temporal dynamics and regulatory activities of each pathway. Single-cell RNA-seq analysis and multiplex immunofluorescence staining in primary PDAC samples further reveal extensive and distinct interactions with components of the tumor microenvironment. Motif analysis of RELA- and RELB-bound regions uncovers a particularly strong association of RELB with AP1 elements. Notably, while RELA binds to both open and closed chromatin, RELB exclusively occupies regions with pre-existing chromatin accessibility and AP1 co-binding. Collectively, these findings underscore the distinct and complementary roles of TNFα and TWEAK in PDAC, with TNFα engaging a broader transcriptional program via RELA and TWEAK selectively targeting genes marked by accessible chromatin and epigenetic activity. This study provides critical insights into the regulatory dynamics of NF-κB signaling in PDAC, highlighting unique and complementary functions of RELA and RELB in modulating downstream gene expression. Significance TNFα and TWEAK selectively activate RELA and RELB in pancreatic cancer, revealing that RELB-driven noncanonical signaling depends on chromatin accessibility and AP-1, uncovering distinct, targetable epigenetic dependencies from canonical signaling. Graphical abstract

Abstract Cutaneous T-cell lymphoma (CTCL) is a rare malignancy of skin-resident T cells characterized by an aberrant cytokine profile, notably elevated Interleukin-17A (IL-17A) levels. However, the functional importance of IL-17A dysregulation in the CTCL pathogenesis remains poorly understood. Our analysis revealed increased IL-17A receptor (IL-17RA) expression in CTCL patient samples, supporting the importance of IL-17A signaling in CTCL progression. Proteomic and metabolomic profiling of IL-17A-treated malignant T cells revealed mitochondrial electron transport chain (ETC) complex I as a key downstream target of IL-17A signaling. Furthermore, we confirmed the elevated expression of ETC complex I in CTCL patient samples compared to healthy control T cells, hence highlighting the clinical relevance of the IL-17A signaling-ETC complex 1 axis. Altogether, our data unveil the function of IL-17A signaling in the metabolic axis in CTCL progression, which could be useful for developing advanced therapeutic strategies. Significance statement: We uncover an IL-17A-induced electron transport chain (ETC) complex I pro-tumorigenic circuit and provide proof of concept evidence that ETC complex I can be targeted to combat the challenges posed by Cutaneous T-cell Lymphoma aggressiveness.

Background/Objectives: Scaphoid fractures are notorious for a high rate of nonunion, resulting in chronic pain and impaired wrist function. The decision for surgical intervention often involves extensive imaging and prolonged conservative management, leading to delays in definitive treatment. The effectiveness of such treatment remains a subject of ongoing clinical debate, with no universally accepted predictive tool for surgical success. The objective of this study was to train a deep learning algorithm to reliably identify cases of nonunion with a high probability of subsequent union following operative revision. Methods: This study utilized a comprehensive database of 346 patients diagnosed with scaphoid nonunions, with preoperative and postoperative X-rays available for analysis. A classical logistic regression for clinical parameters was used, as well as a TensorFlow deep learning algorithm on X-rays. The latter was developed and applied to these imaging datasets to predict the likelihood of surgical success based solely on the preoperative anteroposterior (AP) X-ray view. The model was trained and validated over six epochs to optimize its predictive accuracy. Results: The logistic regression yielded an accuracy of 66.3% in predicting the surgical outcome based on patient parameters. The deep learning model demonstrated remarkable predictive accuracy, achieving a success rate of 93.6%, suggesting its potential as a reliable tool for guiding clinical decision-making in scaphoid nonunion management. Conclusions: The findings of this study indicate that the preoperative AP X-ray of a scaphoid nonunion provides sufficient information to predict the likelihood of surgical success when analyzed using our deep learning model. This approach has the potential to streamline decision-making and reduce reliance on extensive imaging and prolonged conservative treatment.

Abstract Senescent cells drive tissue dysfunction through the senescence-associated secretory phenotype (SASP). We uncovered a central role for mitochondria in the epigenetic regulation of the SASP, where mitochondrial-derived metabolites, specifically citrate and acetyl-CoA, fuel histone acetylation at SASP gene loci, promoting their expression. We identified the mitochondrial citrate carrier (SLC25A1) and ATP-citrate lyase (ACLY) as critical for this process. Inhibiting these pathways selectively suppresses SASP without affecting cell cycle arrest, highlighting their potential as therapeutic targets for age-related inflammation. Notably, SLC25A1 inhibition reduces systemic inflammation and extends healthspan in aged mice, establishing mitochondrial metabolism as pivotal to the epigenetic control of aging.

Abstract Senescent cells secrete proinflammatory factors known as the senescence-associated secretory phenotype (SASP), contributing to tissue dysfunction and aging. Mitochondrial dysfunction is a key feature of senescence, influencing SASP via mitochondrial DNA (mtDNA) release and cGAS/STING pathway activation. Here, we demonstrate that mitochondrial RNA (mtRNA) also accumulates in the cytosol of senescent cells, activating RNA sensors RIG-I and MDA5, leading to MAVS aggregation and SASP induction. Inhibition of these RNA sensors significantly reduces SASP factors. Furthermore, BAX and BAK plays a key role in mtRNA leakage during senescence, and their deletion diminishes SASP expression in vitro and in a mouse model of Metabolic Dysfunction Associated Steatohepatitis (MASH). These findings highlight mtRNA's role in SASP regulation and its potential as a therapeutic target for mitigating age-related inflammation.