Institute of Genetics and Molecular and Cellular Biology

Optimizing radioenhancerdesign for cancer therapy has been limitedby inconsistent metal comparisons and unclear nanoscale mechanisms.High-Z nanoparticles are expected to enhance radiation effects throughincreased photoelectric absorption and secondary electron production,with the common assumption that radioenhancement efficacy increasesuniformly with atomic number. However, this linear relationship maybe oversimplified. Here, we introduce a versatile, supramolecularpeptide platform enabling direct and standardized comparison of gadolinium(Gd), bismuth (Bi), and hafnium (Hf) as radioenhancers within a single,biologically targeted framework. This system is based on autoassembledpeptide heterodimers (E3-K3) incorporating a flexible chelator (DOTAGA)and variable heavy-chain antibody (VHH) domains, ensuring uniformcellular uptake and precise tumor targeting. Systematic invitro and in vivo analyses across HER2+breast cancer and disseminated multiple myeloma models demonstratethat radioenhancement efficacy correlates with atomic number but notin a simple linear fashion, with physicochemical properties of eachmetal determining biological outcomes such as DNA damage induction,reactive oxygen species generation, and clonogenic survival reduction.Specifically, Gd- and Bi-loaded formulations significantly enhancedtumor control under external beam radiotherapy, with Bi exhibitingsuperior efficacy, while Gd-based constructs facilitated MRI-guidedradioligand therapy. Our study elucidates fundamental physical mechanismsgoverning metal-dependent radioenhancement at the nanoscale but alsoestablishes a broadly applicable theranostic approach with significanttranslational implications for personalized radiation oncology.

Mammalian genomes are organized by multi-level folding; yet how this organization contributes to cell-type-specific transcription remains unclear. SATB1 forms a nuclear substructure that resists high-salt extraction. SATB1 binds base-unpairing regions (BURs), genomic elements with high unwinding propensities. In mouse thymocytes, we found that SATB1 establishes a two-tiered chromatin organization: one through indirect binding to transcriptionally active DNase 1-accessible chromatin and another by direct binding to BURs in the DNase 1-inaccessible nuclear substructure. Recently published ChIP-seq datasets show SATB1 binding to accessible chromatin at enhancers and CTCF sites, but not to BURs. By employing urea ChIP-seq, which retains only directly bound protein:DNA complexes, we found that BURs, but not CTCF sites, are direct SATB1 binding targets genome-wide. BURs bound to the SATB1 nuclear substructure interact with accessible chromatin, crossing multiple topologically associated domains (TADs). SATB1 is required for these megabase-scale interactions linked to cell-type-specific gene expression. BURs are highly enriched within transcriptionally repressive lamina-associated domains (LADs). Besides these BURs, SATB1 anchors some BURs (18%) outside LADs near genes in otherwise accessible chromatin to the SATB1 nuclear substructure. Only a subset of total BURs is bound to SATB1, depending on cell type. Notably, despite the mutually exclusive SATB1-binding profiles uncovered by the two ChIP-seq methods, we found most peaks in both profiles are valid and require SATB1. Based on these and previous data, we propose that the SATB1 protein network forms a chromatin scaffold, providing an interface that connects accessible chromatin to a subnuclear architectural structure, thereby facilitating the three-dimensional organization linked to cell-type-specific gene expression.

ABSTRACTBiomedical research data visualization faces several challenges, including insufficient expertise and fragmented methodologies, which severely limit research efficiency and result quality. FigureYa is a standardized visualization framework composed of 317 modular R/python scripts, rather than a standalone software or desktop application. It covers key domains such as expression profiling, immune analysis, survival analysis, and single‐cell data visualization. Based on the concept of “replace data and use,” FigureYa significantly lowers the technical threshold, allowing researchers to generate high‐quality charts without requiring an extensive programming background. Compared to generic online R code snippets, FigureYa offers rigorously developed, thoroughly validated, and biologically contextualized visualization modules originally written by the author team. Each script includes version‐matched environments, example datasets, and detailed annotations, providing clear advantages in automation, reproducibility, and scientific professionalism, thereby providing a standardized visualization solution for complex biomedical data. This innovative tool optimizes research time allocation, promotes interdisciplinary collaboration, accelerates scientific discovery and clinical translation, and provides robust data visualization support for biomedical research.

UFMylation is a Ubiquitin-like post-translational modification involved in myriad of cellular processes. Enzymes involved in this pathway, including ligases and UFM1-specific proteases, are essential for development and homeostasis. Our previous transcriptomic analyses identified an enrichment of Ufsp1 at the neuromuscular junction of skeletal muscle cells. Ufsp1, one of the two UFM1 proteases, had been considered a pseudogene due to truncation of its catalytic domain in several species, including humans. However, recent findings revealed that Ufsp1 is translated from a non-canonical start codon in humans, yielding a catalytically active enzyme. This discovery has revived interest in studying Ufsp1’s role in vivo. We generated two mutant mouse models, one with a point mutation abolishing catalytic activity and another with complete knockout of the gene. Unlike other UFMylation pathway enzymes, both Ufsp1 mutants were born in normal ratios and did not exhibit gross phenotypic abnormalities. Despite the enrichment of Ufsp1 at neuromuscular junctions, only mild structural alterations of this synapse were detected, which did not impact overall muscle function. Our findings indicate that Ufsp1 is dispensable for normal development and homeostasis in mice, but further exploration of its function is needed in pathological conditions.

Transcript buffering entails reciprocal modulation of mRNA synthesis and degradation to maintain stable RNA levels under varying cellular conditions. Current models depict a global connection between mRNA synthesis and degradation, but underlying mechanisms remain unclear. Here, we show that changes in RNA metabolism following depletion of TIP60/KAT5, the acetyltransferase subunit of the NuA4 transcriptional coactivator complex, reveal that transcript buffering occurs at a gene-specific level. By combining RNA sequencing of nuclear, cytoplasmic, and newly synthesized transcript fractions with biophysical modeling in mouse embryonic stem cells, we demonstrate that transcriptional changes caused by TIP60 depletion are offset by corresponding changes in RNA nuclear export and cytoplasmic stability, indicating gene-specific buffering. Disruption of the unrelated ATAC coactivator complex also causes gene-specific transcript buffering. We propose that cells dynamically adjust RNA splicing, export, and degradation in response to individual RNA synthesis alterations, thereby sustaining cellular homeostasis.

ABSTRACT Nucleoporins, essential proteins building the nuclear pore, are pivotal for ensuring nucleocytoplasmic transport. While traditionally confined to the nuclear envelope, emerging evidence indicates their presence in various cytoplasmic structures, suggesting potential non-transport-related roles. This review consolidates findings on cytoplasmic nucleoporin assemblies across different states, including normal physiological conditions, stress, and pathology, exploring their structural organization, formation dynamics, and functional implications. We summarize the current knowledge and the latest concepts on the regulation of nucleoporin homeostasis, aiming to enhance our understanding of their unexpected roles in physiological and pathological processes.

Non-motor aspects in dystonia are now well recognized. The sense of agency, which refers to the experience of controlling one's own actions, has been scarcely studied in dystonia, even though its disturbances can contribute to movement disorders. Among various brain structures, the cerebral cortex, the cerebellum, and the basal ganglia are involved in shaping the sense of agency. In myoclonus dystonia, resulting from a dysfunction of the motor network, an altered sense of agency may contribute to the clinical phenotype of the condition. In this study, we compared the explicit and implicit sense of agency in patients with myoclonus dystonia caused by a pathogenic variant of SGCE (DYT-SGCE) and control participants. We utilized behavioural tasks to assess the sense of agency and performed neuroimaging analyses, including structural, resting-state functional connectivity, and dynamic causal modelling, to explore the relevant brain regions involved in the sense of agency. Additionally, we examined the relationship between behavioural performance, symptom severity, and neuroimaging findings. We compared 19 patients with DYT-SGCE and 24 healthy volunteers. Our findings revealed that patients with myoclonus-dystonia exhibited a specific impairment in explicit sense of agency, particularly when implicit motor learning was involved. However, their implicit sense of agency remained intact. These patients also displayed grey-matter abnormalities in the motor cerebellum, as well as increased functional connectivity between the cerebellum and pre-supplementary motor area. Dynamic causal modelling analysis further identified reduced inhibitory effects of the cerebellum on the pre-supplementary motor area, decreased excitatory effects of the pre-supplementary motor area on the cerebellum, and increased self-inhibition within the pre-supplementary motor area. Importantly, both cerebellar grey-matter alterations and functional connectivity abnormalities between the cerebellum and pre-supplementary motor area were found to correlate with explicit sense of agency impairment. Increased self-inhibition within the pre-supplementary motor area was associated with less severe myoclonus symptoms. These findings highlight the disruption of higher-level cognitive processes in patients with myoclonus-dystonia, further expanding the spectrum of neurological and psychiatric dysfunction already identified in this disorder.

Few studies have considered the influence of motor sign asymmetry on motivated behaviors in de novo drug-naïve Parkinson’s disease (PD). We tested whether motor sign asymmetry could be associated with different motivated behavior patterns in de novo drug-naïve PD. We performed a cross-sectional study in 128 de novo drug-naïve PD patients and used the Ardouin Scale of Behavior in Parkinson’s disease (ASBPD) to assess a set of motivated behaviors. We assessed motor asymmetry based on (i) side of motor onset and (ii) MDS-UPDRS motor score, then we compared right hemibody Parkinson’s disease to left hemibody Parkinson’s disease. According to the MDS-UPDRS motor score, patients with de novo right hemibody PD had significantly lower frequency of approach behaviors (p = 0.031), including nocturnal hyperactivity (p = 0.040), eating behavior (p = 0.040), creativity (p = 0.040), and excess of motivation (p = 0.017) than patients with de novo left hemibody PD. Patients with de novo left hemibody PD did not significantly differ from those with de novo right hemibody PD regarding avoidance behaviors including apathy, anxiety and depression. Our findings suggest that motor sign asymmetry may be associated with an imbalance between motivated behaviors in de novo drug-naïve Parkinson’s disease.