Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction.

Approximately 2.6% of live births in the United States are conceived using assisted reproductive technologies (ARTs). Although some ARTs, including in vitro fertilization (IVF) and intracytoplasmic sperm injection, are known to alter the epigenetic landscape of early embryonic development, their impact on DNA sequence stability is unclear. Here, we leverage the strengths of the laboratory mouse model system to investigate whether a standard ART series (ovarian hyperstimulation, gamete isolation, IVF, embryo culture, and embryo transfer) affects genome stability. Age-matched cohorts of 12 ART-derived and 16 naturally conceived C57BL/6J inbred mice were reared in a controlled setting and whole-genome-sequenced to ∼50× coverage. Using a rigorous pipeline for de novo single-nucleotide variant (dnSNV) discovery, we observe a ∼30% (95% CI: 4.5%–56%) increase in the dnSNV rate with ART compared with naturally conceived mice (P = 0.017). Analysis of the dnSNV mutation spectrum identifies signatures attributable to germline DNA repair activity but reveals no differentially enriched signatures between cohorts. We observe no enrichment of dnSNVs in specific genomic contexts, suggesting that the observed rate increase in ART-derived mice is a general genome-wide phenomenon. Together, our findings show that ART is moderately mutagenic in house mice and motivate future work to define the procedure(s) associated with this increased mutational vulnerability. Although we caution that our findings cannot be immediately translated to humans, they nonetheless emphasize a pressing need for investigations on the potential mutagenicity of ART in our species

Perspectives from the 2025 ISCBI/ISCI joint workshop on genetic stability, clonal monitoring, ethical data governance, and global inclusion in stem cell banking.

Two international stem cell consortia, the International Stem Cell Initiative (ISCI) and the International Stem Cell Biobanking Initiative (ISCBI, www.iscbi.org ) held a workshop on June 15th 2025 in Hong Kong on genetic variants in human pluripotent stem cell (hPSC) lines and accurate and standardized documentation of donor/hPSC genetic information including ethnicity. The occurrence and detection of genetic variants is a key issue for assuring reproducible stem cell research data and the safety of stem cell derived medicinal products. Presentations by leading experts addressed the nature of hPSC genetic variants, their detection and accurate recording of genetic data and ethnicity. The audience of stem cell researchers, cell banking directors and experts in ethic, policy and stem cell databases, from 13 countries across the globe, discussed progression of the ISCI consortium\u27s efforts in providing further data and thought leadership on the management of genetic variants, and the challenges for standardizing biobanking approaches for hPSC genetic data including ethnicity. This paper records the key elements of this discussion and the conclusions and consensus reached and ongoing work to provide guidance for hPSC biobanks

An ITPR1 Variant in the IP3-ITPR1 Binding Pocket Associated With a Clinical Phenotype of Athetoid Cerebral Palsy.

A de novo, missense variant in ITPR1-inositol 1,4,5-trisphosphate receptor type 1 (ITPR1), p.(Tyr567Cys), was identified by trio whole-genome sequencing in an individual diagnosed with Spinocerebellar ataxia 29 (SCA29) who was affected by cerebral palsy and global developmental delay. The variant affects a residue involved in Inositol 1,4,5-trisphosphate (IP3)-ITPR1 binding. Genotype-Phenotype correlation analysis of the set of missense variants affecting nine residues involved in IP3-ITPR1 binding in the current case and 170 reports of individuals with ITPR1 variants showed a significantly higher frequency of phenotypic features related to neurodevelopmental delay in these variants than in other ITPR1 variants. Our proband was diagnosed with cerebral palsy, as were five other published individuals diagnosed with SCA29. Two of these individuals were siblings who were found to have the variant p.(Arg269Trp), also located in the IP3-ITPR1 binding pocket. These observations suggest that genotype-phenotype correlations exist in the ITPR1 gene and underscore the importance of data sharing and reuse to elucidate the natural history of rare neurodevelopmental diseases

Overcoming EGFR-Mediated Dendritic Cell Dysfunction to Enhance Anti-tumor Immunity in EGFR-Mutant NSCLC by Precisely Targeting CD73 With pH-responsive Nanocarriers.

EGFR mutations remain a major challenge in immunotherapy for non-small cell lung cancer (NSCLC), with poor responses to immune checkpoint inhibitors driven by mechanisms associated with EGFR mutation-mediated tumor microenvironment (TME) modulation. This study reveals that EGFR mutations prominently impaired dendritic cell (DC) maturation, disrupting their capacity to effectively prime CD8+ T cells and thereby compromising anti-tumor immune responses. By application of clinical specimen analyses, multi-omics approaches, and in vivo mouse models, this work demonstrates that EGFR mutations elicited adenosine production through the ERK/c-Jun signaling axis in tumor cells, establishing an immunosuppressive TME that impeded maturation and antigen presentation of DCs, and in turn weakened CD8+ T cell activation. To overcome the EGFR mutation-induced immunosuppression, this work next develops F127 ZIF-8 AB680 , a pH-responsive and tumor-selective nanodrug specifically designed to target the CD73-adenosine pathway within the acidic TME. This nanodrug significantly improves the therapeutic efficacy of PD-1 blockade, leading to robust tumor growth inhibition and prolonged survival of mice in EGFR-mutant NSCLC models. Leveraging the advanced nanotechnology, this newly designed pH-sensitive nanocarrier introduces a precise CD73/adenosine inhibition within the acidic TME that reprograms the immune landscape in EGFR-mutant NSCLC, which represents a promising therapeutic strategy to overcome immunotherapy resistance in NSCLC

Educational efficacy of training videos and simulators for teaching basic mouse experimental skills to novice veterinary students.

Alternative educational tools, such as training videos and simulators, are recommended in the education of laboratory animal science. However, evidence supporting their educational utility in the training of rodent experimental techniques remains limited. In this study, we assessed the utility of alternative educational tools in the practice of laboratory animal science for novice veterinary students. 149 students participated in a stepwise program beginning with lectures, followed by preparatory learning sessions using training videos and two types of mouse simulators (a silicone-based model and fabric toy mouse), and then hands-on training with live mice. The program covered basic techniques: habituation, restraint, and vaginal smear sampling for estrous cycle determination. A survey-based evaluation was conducted to assess the educational utility of alternative educational tools. The contribution of each preparatory resource (videos, lectures, simulators, printed materials, and notes) to skill acquisition was evaluated, showing that videos, lectures, and printed materials highly contributed. The training videos were rated as more necessary than the simulators for skill acquisition. Psychological evaluation showed that 84% of students experienced anxiety before practice. A positive correlation was found between anxiety levels and frequency of use for all three tools, and students reported that all tools were effective in reducing anxiety during practice. All techniques showed high proficiency rates. Our findings suggest that integrating alternative tools with live-animal training promotes technical skill acquisition, enhances psychological readiness, and supports 3Rs-based laboratory animal practice

From gene modules to gene markers: an integrated AI-human approach selects CD38 to represent plasma cell-associated transcriptional signatures.

BACKGROUND: Knowledge-driven prioritization of candidate genes derived from large-scale molecular profiling data for targeted transcriptional profiling assays is challenging due to the vast amount of biomedical literature that needs to be harnessed. We present a workflow leveraging Large Language Models (LLMs) to prioritize candidate genes within module M12.15, a plasma cell-associated module from the BloodGen3 repertoire, by integrating knowledge-driven prioritization with data-driven analysis of transcriptome profiles. METHODS: The workflow involves a two-step process: (1) high-throughput screening using LLMs to score and rank the 17 genes of module M12.15 based on six predefined criteria, and (2) prioritization employing high-resolution scoring and fact-checking, with human experts validating and refining AI-generated scores. RESULTS: The first step identified five candidate genes (CD38, TNFRSF17, IGJ, TOP2A, and TYMS). Following human-augmented LLM scoring and fact checking, as part of the second step, CD38 and TNFRSF17 emerged as the top candidates. Next, transcriptome profiling data from three datasets was incorporated in the workflow to assess expression levels and correlations with the module average across various conditions and cell types. It is on this basis that CD38 was prioritized as the top candidate, with TNFRSF17 and IGJ identified as promising alternatives. CONCLUSION: This study introduces a systematic framework that integrates LLMs with human expertise for gene prioritization. Our analysis identified CD38, TNFRSF17, and IGJ as the top candidates within the plasma cell-associated module M12.15 from the BloodGen3 repertoire, with their relative rankings varying systematically based on specific evaluation criteria, from plasma cell biology to therapeutic relevance. This criterion-dependent ranking demonstrates the ability of the framework to perform nuanced, multi-faceted evaluations. By combining knowledge-driven analysis with data-driven metrics, our approach provides a balanced and comprehensive method for biomarker selection. The methodology established here offers a reproducible and scalable approach that can be applied across diverse biological contexts and extended to analyze large module repertoires

Analysis of functional connectivity changes from childhood to old age: A study using HCP-D, HCP-YA, and HCP-A datasets.

We present a new clustering-enabled regression approach to investigate how functional connectivity (FC) of the entire brain changes from childhood to old age. By applying this method to resting-state functional magnetic resonance imaging data aggregated from three Human Connectome Project studies, we cluster brain regions that undergo identical age-related changes in FC and reveal diverse patterns of these changes for different region clusters. While most brain connections between pairs of regions show minimal yet statistically significant FC changes with age, only a tiny proportion of connections exhibit practically significant age-related changes in FC. Among these connections, FC between region clusters from the same functional network tends to decrease over time, whereas FC between region clusters from different networks demonstrates various patterns of age-related changes. Moreover, our research uncovers sex-specific trends in FC changes. Females show much higher FC mainly within the default mode network, whereas males display higher FC across several more brain networks. These findings underscore the complexity and heterogeneity of FC changes in the brain throughout the lifespan

Amyotrophic lateral sclerosis and frontotemporal dementia mutation reduces endothelial TDP-43 and causes blood-brain barrier defects.

Mutations in the TARDBP gene encoding TDP-43 protein are linked to loss of function in neurons and familial frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). We recently identified reduced nuclear TDP-43 in capillary endothelial cells (ECs) of donors with ALS-FTD. Because blood-brain barrier (BBB) permeability increases in ALS-FTD, we postulated that reduced nuclear TDP-43 in ECs might contribute. Here, we show that nuclear TDP-43 is reduced in ECs of mice with an ALS-FTD–associated mutation in TDP-43 (TardbpG348C) and that this leads to cell-autonomous loss of junctional complexes and BBB integrity. Targeted excision of TDP-43 in brain ECs recapitulates BBB defects and loss of junctional complexes and ultimately leads to fibrin deposition, gliosis, phospho-Tau accumulation, and impaired memory and social interaction. Transcriptional changes in TDP-43–deficient ECs resemble diseased brain ECs. These data show that nuclear loss of TDP-43 in brain ECs disrupts the BBB and causes hallmarks of FTD

Spatiotemporal Profiling Defines Persistence and Resistance Dynamics during Targeted Treatment of Melanoma.

Resistance of BRAF-mutant melanomas to targeted therapy arises from the ability of cells to enter a persister state, evade treatment with relative dormancy, and repopulate the tumor when reactivated. A better understanding of the temporal dynamics and specific pathways leading into and out of the persister state is needed to identify strategies to prevent treatment failure. Using spatial transcriptomics in patient-derived xenograft models, we captured clonal lineage evolution during treatment. The persister state showed increased oxidative phosphorylation, decreased proliferation, and increased invasive capacity, with central-to-peripheral gradients. Phylogenetic tracing identified intrinsic and acquired resistance mechanisms (e.g., dual-specific phosphatases, reticulon-4, and cyclin-dependent kinase 2) and suggested specific temporal windows of potential therapeutic susceptibility. Deep learning-enabled analysis of histopathologic slides revealed morphologic features correlating with specific cell states, demonstrating that juxtaposition of transcriptomics and histologic data enabled identification of phenotypically distinct populations from using imaging data alone. In summary, this study defined state change and lineage selection during melanoma treatment with spatiotemporal resolution, elucidating how choice and timing of therapeutic agents will impact the ability to eradicate resistant clones. Significance: Tracking clonal progression during treatment uncovers conserved, global transcriptional changes and local clone-clone and spatial patterns underlying the emergence of resistance, providing insights into therapy-induced tumor evolution