Fleet Science Center

Abstract Retrospective reconstruction of cell lineages from somatic mutations holds substantial promise for understanding development, tissue homeostasis, and disease. Yet, current approaches are often constrained by low marker density, technical noise, and incomplete molecular readouts that limit the resolution and accuracy of inferred lineages. Here, we present RETrace2, a single-cell dual-omic method for simultaneous lineage tracing and cell-type identification. By identifying and targeting highly mutable homopolymers, which we show are approximately twice as informative as conventional microsatellite repeats, combined with technical improvements to increase marker coverage and reduce experimental errors of reading and amplifying homopolymers, RETrace2 can trace lineage continuously at an estimated resolution of fewer than five cell divisions in microsatellite-unstable organisms. Simultaneously, sparse methylation profiles were obtained from the same cells for cell-type identification. We validated the method using in vitro ground-truth models and demonstrated its utility in vivo by reconstructing multi-organ lineage trees from the brain, kidney and liver of Msh2 -deficient mice.

Teprotumumab, a monoclonal antibody targeting the insulin-like growth factor-1 receptor, has demonstrated significant efficacy in treating thyroid eye disease. While its ophthalmic benefits are well established, limited data exist regarding its effects on thyroid hormone regulation. To characterize changes in thyroid function associated with teprotumumab therapy in thyroid eye disease patients. We performed a retrospective comparative study of 46 thyroid eye disease patients treated with teprotumumab and 46 thyroid eye disease patients treated with orbital decompression at a tertiary care facility between January 2020 and December 2023. Thyroid function tests (thyroid-stimulating hormone and free thyroxine) were analyzed at pretreatment and posttreatment. Subgroup analysis was conducted based on prior thyroidectomy or radioactive iodine therapy. Clinical outcomes, including proptosis and Clinical Activity Score, were also evaluated. The teprotumumab cohort had a mean age of 55.9 years, with 80.5% female and 65.2% hyperthyroid at presentation. The orbital decompression cohort mean age was 49.8 years, with 89.1% female and 80.4% hyperthyroid. Both groups showed significant improvements in Clinical Activity Score and proptosis. In the teprotumumab group, free thyroxine levels significantly declined posttreatment (1.7 ± 1.2 to 1.3 ± 0.4, p = 0.049), particularly in patients without prior thyroidectomy/radioactive iodine (1.8 ± 1.4 to 1.2 ± 0.3, p = 0.041). The orbital decompression group showed no significant change in free thyroxine levels (p = 0.63). Over half (52.2%) of teprotumumab patients required medication adjustments during therapy, compared with 12.5% in the orbital decompression group (p < 0.001). Teprotumumab may impact thyroid hormone homeostasis, especially in patients with functioning thyroid tissue, suggesting a need for endocrine monitoring with treatment.

Proteostasis supports stemness, and its loss correlates with the functional decline of diverse stem cell types. Chaperone-mediated autophagy (CMA) is a selective autophagy pathway implicated in proteostasis, but whether it plays a role in muscle stem cell (MuSC) function is unclear. Here we show that CMA is necessary for MuSC regenerative capacity throughout life. Genetic loss of CMA in young MuSCs, or failure of CMA in aged MuSCs, causes proliferative impairment resulting in defective skeletal muscle regeneration. Using comparative proteomics to identify CMA substrates, we find that actin cytoskeleton organization and glycolytic metabolism are key processes altered in aged murine and human MuSCs. CMA reactivation and glycolysis enhancement restore the proliferative capacity of aged mouse and human MuSCs, and improve their regenerative ability. Overall, our results show that CMA is a decisive stem cell-fate regulator, with implications in fostering muscle regeneration in old age.

For a drug candidate to make it past the preclinical trial stage, mutagenicity must be ruled out. In the preclinical pipeline, drug mutagenicity is assessed using the Salmonella/microsome mutagenicity assay, colloquially called the Ames test. In nearly all instances, the FDA necessitates the Ames test for IND submission and drug approval. Difficult to scale up, the Ames test has given way to artificial intelligence (AI)-driven computational alternatives, which predict strain-specific Ames mutations in quantitative structure-activity relationship (QSAR) experiments. Reported in a recent study, a multitask Ames QSAR algorithm, which predicts eight strain-specific mutations, matched state-of-the-art performance as measured by balanced accuracy. But, like most other neural network applications used to predict Ames genotoxicity, these multitask algorithms struggle with sensitivity and fail to generalize efficiently to out-of-domain data. We recently developed ChemPrint, a molecular geometric convolutional neural network, which generalizes well to out-of-domain data. Validated across multiple protein targets in our drug discovery programs, ChemPrint achieved a 46% (19/41) zero-shot hit rate in our AXL and BRD4 oncology program, a 100% (12/12) one-shot hit rate in our RdRp Thumb-1 antiviral program, and enabled off-target binding reductions ranging from 800-fold to over 15,000-fold. We report here AmesNet, an adaptation of ChemPrint, which predicts strain-specific Ames mutations. AmesNet learns from the concatenation of ChemPrint's molecular embeddings with Ames mutagenicity features. When benchmarked against leading Ames QSAR algorithms, AmesNet achieves state-of-the-art balanced accuracy and sensitivity across both in-domain and out-of-domain data. AmesNet attained a sensitivity of 0.75, marking a 30% improvement over the best-performing ML method on the test set. AmesNet is embedded in GALILEO, our AI-based drug discovery platform. The GALILEO ecosystem, which also includes bioinformatics and generative chemistry tools, will continue to grow. ChemPrint and AmesNet are the beginning in a series of AI tools that will greatly accelerate and derisk the drug discovery pipeline, by predicting every aspect of the drug safety landscape assessed in the preclinical setting-absorption, distribution, metabolism, excretion, and toxicity (ADMET).

This study evaluates the clinical presentation, surgical management, and outcomes of silent sinus syndrome (SSS), with emphasis on the efficacy of simultaneous sinus and orbital surgery. A retrospective review was performed of 35 patients diagnosed with SSS at a tertiary care center between January 2004 and April 2024. All patients had radiographic evidence of maxillary sinus atelectasis and orbital floor resorption. Management strategies included observation (n=12), sinus surgery alone (n=10), simultaneous endoscopic sinus surgery with orbital reconstruction (n=12), and staged procedures (n=1). The most common presenting signs were enophthalmos (48.5%), hypoglobus (37.1%), and diplopia (11.4%). Patients undergoing simultaneous repair demonstrated significant improvement in enophthalmos compared with preoperatively (from 3.2±1.1 to 0.6±0.5mm, P =0.0002) and hypoglobus (from 2.6±1.0 to 0.1±0.5mm, P <0.0001) and compared with those treated with sinus surgery alone (postoperative enophthalmos 2.5±0.7mm, P =0.005). No cases of implant extrusion, infection, or vision loss were observed. Complications were limited to 1 case of transient infraorbital hypesthesia and 1 case of hyperglobus requiring revision. These findings suggest that single-stage combined sinus surgery with orbital reconstruction is safe and effective for restoring globe position in patients with SSS and clinically significant orbital displacement.

Circadian rhythmicity of gene expression is a conserved feature of cell physiology. This involves fine-tuning between transcriptional and post-transcriptional mechanisms and strongly depends on the metabolic state of the cell. Together these processes guarantee an adaptive plasticity of tissue-specific genetic programs. However, it is unclear how the epigenome and RNA Pol II rhythmicity are integrated. Here we show that the PcG protein EZH1 has a gateway bridging function in postmitotic skeletal muscle cells. On the one hand, the circadian clock master regulator BMAL1 directly controls oscillatory behavior and periodic assembly of core components of the PRC2–EZH1 complex. On the other hand, EZH1 is essential for circadian gene expression at alternate Zeitgeber times, through stabilization of RNA Polymerase II preinitiation complexes, thereby controlling nascent transcription. Collectively, our data show that PRC2–EZH1 regulates circadian transcription both negatively and positively by modulating chromatin states and basal transcription complex stability.

The author group has been updated above and the original article has been corrected.

ObjectiveTo quantify the observed decrease in orbital decompressions being performed at one tertiary care institution and to determine the rate and predictive factors of orbital decompression surgery following treatment with teprotumumab for thyroid eye disease. MethodsEpic's SlicerDicer program was used to analyze recent trends in the overall number of thyroid eye disease (TED) patients evaluated in the oculoplastic surgery department, as well as usage trends of CPT codes 67445 (lateral orbitotomy with bone removal for decompression) and 67414 (orbitotomy with removal of bone for decompression). A retrospective chart review of active moderate-to-severe TED patients treated with teprotumumab was performed at a single tertiary care center. The main outcome measure was whether or not patients underwent bony orbital decompression surgery following treatment with teprotumumab. The SlicerDicer search demonstrated stable usage of CPT codes 67445 and 67414 from 2016 to 2019, followed by a significant decrease from 2020 to 2023, over a background of increasing numbers of TED patients evaluated in clinic. Following teprotumumab therapy, 25% of patients and 18% of orbits underwent bony decompression. Surgically decompressed patients had higher pre- and post-teprotumumab exophthalmometry measurements compared with patients who did not undergo bony decompression. Average time to decompression following conclusion or cessation of teprotumumab therapy was 12.6 months. ConclusionWhile the number of TED patients treated at one tertiary care center has risen over recent years, the number of orbital decompression surgeries has declined. Orbital decompression, however, is still needed in select patients after treatment with teprotumumab.

BackgroundHeterogeneity in ageing rates drives the need for research into lifestyle secrets of successful agers. Biological age, predicted by epigenetic clocks, has been shown to be a more reliable measure of ageing than chronological age. Dietary habits are known to affect the ageing process. However, much remains to be learnt about specific dietary habits that may directly affect the biological process of ageing.ObjectiveTo identify food groups that are directly related to biological ageing, using Copula Graphical Models.MethodsWe performed a preregistered analysis of 3,990 postmenopausal women from the Women’s Health Initiative, based in North America. Biological age acceleration was calculated by the epigenetic clock PhenoAge using whole-blood DNA methylation. Copula Graphical Modelling, a powerful data-driven exploratory tool, was used to examine relations between food groups and biological ageing whilst adjusting for an extensive amount of confounders. Two food group–age acceleration networks were established: one based on the MyPyramid food grouping system and another based on item-level food group data.ResultsIntake of eggs, organ meat, sausages, cheese, legumes, starchy vegetables, added sugar and lunch meat was associated with biological age acceleration, whereas intake of peaches/nectarines/plums, poultry, nuts, discretionary oil and solid fat was associated with decelerated ageing.ConclusionWe identified several associations between specific food groups and biological ageing. These findings pave the way for subsequent studies to ascertain causality and magnitude of these relationships, thereby improving the understanding of biological mechanisms underlying the interplay between food groups and biological ageing.