bluuebunny/crossref_metadata_2025 huggingface dataset:
Binding affinities for 2D protein dimerization benefit from enthalpic stabilization
Authors: Jhaveri Adip , Chhibber Smriti , Kulkarni Nandan , Johnson Margaret E
Published: January 2025

The binding free energy between a protein dimer and its unbound monomers is primarily quantified in solution (3D), but several classes of soluble proteins, including those containing BAR domains, can also reversibly dimerize while bound to a membrane surface (2D). This 2D assembly process cannot be assigned the same free energy as in 3D due to restrictions to orientational motion and translation normal to the surface. The resulting ratio of dissociation constants,, defines a lengthscale that is essential for determining whether dimerization is more favorable in solution or on the membrane surface. We show here using Molecular Dynamics simulations that changes to configurational sampling of even moderately flexible proteins can significantly alter the free energy landscape from 3D to 2D via not only the expected entropic restrictions, but due to enthalpic gains in the 2D bound ensemble. We simulated homodimerization between BAR-domain containing proteins in three distinct environments: in solution (3D), when bound to a lipid bilayer (2D), and when fully solvated but restrained to a pseudomembrane (2D). The free energy surfaces of both 2D systems are highly distinct from the 3D FES, selecting significantly better for the specific bound structure. We show that this is driven by stabilization of a new ensemble of monomer configurations that result in more enthalpically stable dimers states. Remarkably, performing this same procedure for a distinct parameterization of the BAR domain dimer shows much better agreement between the 3D and 2D FES, and this is supported by overall similarities in the enthalpies in both environments, highlighting the dependence of the FES on molecular structures. Withratios calculated here in the nanometer and lower regime for both dimers, at physiologic volume-to-surface-area ratios these proteins will both produce substantially more dimers on the membrane, which evolutionarily agrees with their function as membrane remodelers.
Intersecting Transcriptomic Landscapes of Hypertension and Kidney Function in African American Women
Authors: Abbas Malak , Martin Pamela , Lindsey Merry , Bennett Eric S. , Brown Thomas L. , Nzerue Chike , Williams Clintoria R. , Gaye Amadou
Published: January 2025

Background

Hypertension is a major risk factor for chronic kidney disease (CKD) and disproportionately affects African American women, contributing to disparities in kidney health outcomes. The biological mechanisms connecting hypertension to reduced kidney function, particularly in understudied populations, remain poorly understood. This study leverages transcriptomic analyses to uncover shared molecular signatures associated with hypertension and kidney function, focusing on female-specific profiles.

Methods

The study analyzed whole-blood mRNA sequencing data from a cohort of 344 African American women, divided equally into discovery (n = 172) and validation (n = 172) datasets, along with 147 African American men. Differential expression (DE) analyses were performed to identify mRNAs associated with hypertension and kidney function (measured as eGFR). Female-specific findings were determined by comparing results between females and males. Pathway enrichment analyses were subsequently conducted to link the identified mRNAs to key biological mechanisms.

Results

Comparative analyses revealed unique transcriptomic profiles in females, underscoring the role of sex-specific factors in disease progression. DE analyses identified 95 female-specific genes associated with both hypertension and eGFR. Subsequent pathway enrichment analysis with the 95 genes revealed key pathways related to fibrosis, inflammation, lipid metabolism, and endothelial dysfunction. The list of 95 includes TGF-β1 and PNPLA2 implicated in fibrotic and metabolic dysregulation, and immune system players such as IL32 and TNFSF12 that amplify inflammation and kidney injury.

Conclusions

This study provides novel insights into the transcriptomic mechanisms underlying hypertension and kidney function in African American women. The findings emphasize the importance of addressing sex-specific and population-specific molecular mechanisms to inform precision medicine approaches and reduce health disparities hypertension-related impaired kidney function. Future research should prioritize experimental validation and longitudinal studies to further elucidate these pathways.
Does sample size of leaf osmotic potential affect its relationship with cotton yield?
Authors: Dong Xuejun , Mott Dale A. , Zhou Quan , McKnight Benjamin M.
Published: January 2025

Leaf osmotic potential at full turgor (π0) has been used frequently to indicate turgor loss point of plant leaves. However, even a rapid measurement ofπ0using osmometry is time-consuming, if numerous leaf samples need to be measured. Because of this, researchers tend to use a small sample size to determineπ0and relate it to indices of crop performance. Yet the statistical and agronomic significance of using a small sample size ofπ0to indicate crop performance is not known. We address this question using field measurements and statistical resampling. Six mature leaf samples were collected at the peak bloom stage from each of the 54 cotton plots in Texas, USA in 2024. Theπ0of the collected leaves were measured using an osmometer. Seed cotton yields from the field plots were measured near the end of cotton season. To test the effect of sample size on strength of the linear relation betweenπ0and cotton yield, 1-6 resamples ofπ0were randomly drawn with replacement from the original 6 measurements per plot for the 54 plots. The resampled data ofπ0were then used as independent variable to predict cotton yield. We found that, considering the labor and cost, sampling 3 or 6 leaves per plot may not make a significant difference for the linear regression betweenπ0and cotton yield.
Oral-stomach sampling to replace rumen-fistulated animals in ruminant nutrition research - a case study
Authors: Boudon A. , Kwiatkowski D. , Niderkorn V. , Forano E. , Nozière P. , Silberberg M.
Published: January 2025

Studies using fistulated ruminants have shed light on digestion and fermentation in the rumen and yielded tools to determine the feed efficiency of diets, limit effluents or anticipate variability in the quality of animal products. However, the ethical acceptability of such studies has been called into question. Our objective was to determine whether oral-stomach sampling (OSS) is an acceptable alternative to sampling through a ruminal cannula in characterizing the variability of rumen fluid composition induced by an acidogenic dietary challenge in dairy cows. During three four-week periods (P1, P2, P3), six rumen-fistulated cows were fed a standard diet based on supplemented corn silage (periods 1 and 3) alternating with a diet enriched with starch (period 2). Rumen juice was collected through cannulas at three locations in the rumen (reticulum, ventral sac or a mix of both) and by OSS, once per week at 0830 h, i.e. before morning feeding, and once every third week of each period at 1330 h, i.e. 4.5 hours after morning feeding. Whatever the sampling method or location, ruminal pH was lower in period 2 compared to periods 1 and 3 at 1330 h (6.21 vs. 5.57 vs. 6.12 in periods 1, 2 and 3). Ruminal pH was higher when obtained by OSS rather than cannulation, whatever the sampling location (on average, +0.44 points at 0830 h and +0.56 points at 1330 h). Mineral composition indicated a presumed dilution by saliva of OSS samples. This was also consistent with lower concentrations of volatile fatty acids. The next steps will be to analyze the associated variations in in vitro rumen fermentation parameters and microbiota composition.

Implications

The use of fistulated ruminants to elucidate ruminal physiology is currently controversial in society. In order to minimise, reduce or replace these experimental models, alternatives to ruminal fistula sampling are being evaluated. Here we focus on oral stomach sampling (OSS). We show that OSS can be a satisfactory alternative to cannula sampling in the evaluation of rumen fermentation parameters, especially for the molar proportion of volatile fatty acids, rumen pH, and rumen volatile fatty acid and ammonia concentrations. We also show that OSS must be standardized to avoid salivary contamination affecting the quality of the results.
Comparative evaluation of computational methods for reconstruction of human viral genomes
Authors: Sousa Maria J. P. , Toppinen Mari , Pyöriä Lari , Hedman Klaus , Sajantila Antti , Perdomo Maria F. , Pratas Diogo
Published: January 2025

The increasing availability of viral sequences has led to the emergence of many optimized viral genome reconstruction tools. Given that the number of new tools is steadily increasing, it is complex to identify functional and optimized tools that offer an equilibrium between accuracy and computational resources as well as the features that each tool provides. In this paper, we surveyed open-source computational tools (including pipelines) used for human viral genome reconstruction, identifying specific characteristics, features, similarities, and dissimilarities between these tools. For quantitative comparison, we create an open-source reconstruction benchmark based on viral data. The benchmark was executed using both synthetic and real datasets. With the former, we evaluated the effects to the reconstruction process of using different human viruses with simulated mutation rates, contamination and mitochondrial DNA inclusion, and various coverage depths. Each reconstruction program was also evaluated using real datasets, demonstrating their performance in real-life scenarios. The evaluation measures include the identity, a Normalized Compression Semi-Distance, and the Normalized Relative Compression between the genomes before and after reconstruction, as well as metrics regarding the length of the genomes reconstructed, computational time and resources spent by each tool. The benchmark is fully reproducible and freely available athttps://github.com/viromelab/HVRS.
The Impact of a Western Diet High in Phosphate on the CKD-MBD in an Alport Syndrome Model
Authors: Williams Matthew J. , Patel Hiral M. , Halling Carley B. , Hruska Keith A.
Published: January 2025

Background

Chronic kidney disease – mineral bone disorder (CKD-MBD) is a syndrome that begins early in CKD, contributes to CKD-associated mortality, and includes components of FGF23 elevation, αklotho deficiency, CKD-stimulated vascular disease, and renal osteodystrophy. Hyperphosphatemia, occurring in later stages of CKD, is also driven by mechanisms of CKD-MBD, and has been shown to stimulate vascular calcification. In a mouse model of Alport CKD that is resistant to vascular calcification, we examine the effects of a high-phosphate Western-type diet on the CKD-MBD, and test whether the diet promotes induction of vascular calcification.

Methods

An X-linked Col4a5 deficient murine homolog of Alport Syndrome (CKD) and wild type (WT) littermates were fed an animal protein 1.2% high phosphate diet or a standard vegetable protein diet. At disease progression equivalent to CKD stage 4-5, we examined kidney histology for fibrosis, blood for BUN (marker of CKD), and markers of CKD-MBD disease progression, kidney tissue for klotho production, and aorta histology and tissue mRNA and protein analysis for vascular calcification.

Results

The Western high Pi diet produced hyperphosphatemia in the CKD animals compared to WT and increased plasma PTH (1880 from 110 pg / ml), FGF23 c-term (670 from 120 pg / ml), and FGF23 intact (3780 from 280 pg / ml), and reduced kidney klotho mRNA and protein (57-67% reduction) (all p < 0.01). Referenced against the CKD animals fed vegetable-based diet, the Western high phosphate-fed CKD animals showed higher levels of plasma PTH and FGF23s. In the wild-type control mice with normal renal function, Western diet produced increased PTH, intact FGF23, and reduced renal klotho (all p <0.01). Vascular smooth muscle transdifferentiation and vascular calcification was not induced by Western high phosphate diet in this model of CKD.

Conclusions

Our results show that a Western-style high-phosphate diet advances elements of the CKD-MBD. Renal klotho, FGF23 and PTH are affected by diet even with normal kidney function, suggesting a need for early intervention in the management of phosphate homeostasis as a component of CKD therapy. Additionally, CKD, klotho, and FGF23 all are associated with early aging. Therefore, our findings suggest that a Western high Pi diet accelerates aging and would contribute to the systemic complications of CKD – cardiac disease, osteodystrophy, and vascular disease.
CYP722A1-driven 16-hydroxylation of carlactonoic acid regulates the floral transition in Arabidopsis
Authors: Kuno Masaki , Miyamoto Ayumi , Takano Hinako , Homma Masato , Shiotani Nanami , Uchida Kiyono , Takikawa Hirosato , Nakajima Masatoshi , Mizutani Masaharu , Wakabayashi Takatoshi , Sugimoto Yukihiro
Published: January 2025

Strigolactones (SLs) are multifunctional plant hormones and rhizosphere signals with diverse structures, broadly categorized as canonical or noncanonical SLs. InArabidopsis thaliana, SL biosynthesis mutants exhibit increased shoot branching and early flowering, underscoring their roles in developmental regulation. Shoot branching inhibition in Arabidopsis depends on the methylation of carlactonoic acid (CLA), a key intermediate classified as a noncanonical SL, catalyzed by CLA methyltransferase (CLAMT). Canonical SLs primarily function as rhizosphere signals, with their biosynthesis in dicots mediated by CYP722C enzymes. It is hypothesized that Arabidopsis does not produce canonical SL because of the lack of theCYP722Cgenes in its genome. Instead, Arabidopsis possesses CYP722A1, a member of the previously uncharacterized CYP722A subfamily, distinct from the CYP722C subfamily.

This study demonstrates that Arabidopsiscyp722a1mutants exhibit an earlier floral transition without excessive shoot branching. Biochemical analysis revealed that CYP722A1 catalyzes the hydroxylation of CLA to produce 16-hydroxy-CLA (16-HO-CLA), which is subsequently methylated by CLAMT to form 16-HO-MeCLA. 16-HO-CLA and 16-HO-MeCLA were detected in the wild-type; however, these compounds were absent inmax1-4mutant, which is deficient in CLA synthesis, and incyp722a1mutant. These findings indicate the presence of CYP722A1-dependent 16-hydroxylation activity of CLA in Arabidopsis. Moreover, they suggest that hydroxylated CLA specifically regulates floral transition, distinct from branching inhibition. By identifying CYP722A1 as a regulator of floral transition, which is the distinct role of the CYP722A subfamily, this work provides insights into the adaptation of SL structures for specialized biological functions in plant development.
Macrophages restrict tumor permissiveness to immune infiltration by controlling local collagen topography through a Tcf4-Collagen3 fibrotic axis
Authors: Fusilier Zoé , Simon Franck , Calvente Isabel , Crestey Lou , Clément Alexandra , Mathieu Mathilde , Jean-Marie Roude , Piastra-Facon Florence , George Clément Jeyani , Lumineau Enola , Tonani Mattia , Manriquez Valeria , Lacerda Livia , de Villemagne Perrine , Piaggio Eliane , Semetey Vincent , Coscoy Sylvie , Martini Emanuele , Scita Giorgio , Gelly Jean-Christophe , Ivaska Johanna , Isambert Hervé , Goudot Christel , Pierobon Paolo , Lennon-Duménil Ana-Maria , Moreau Hélène D.
Published: January 2025

During tumorigenesis, the extracellular matrix (ECM), which constitutes the structural scaffold of tissues, is profoundly remodeled. While the impact of such remodeling on tumor growth and invasion has been extensively investigated, much less is known on the consequences of ECM remodeling on tumor infiltration by immune cells. By combining tissue imaging and machine-learning, we here show that the localization of T lymphocytes and neutrophils, which orchestrate antitumor immune responses, can be predicted by defined topographical features of fibrillar collagen networks. We further show that these collagen topographies result from the activation of a fibrotic pathway controlled by the transcription factor Tcf4 upon depletion of tumor-associated macrophages at late tumor stages. This pathway promotes the deposition of collagen 3 by both tumor and stromal cells, resulting in intermingled collagen networks that favor intra-tumoral T cell and neutrophil localization. Importantly, analysis of human colorectal cancer public bulk RNAseq databases showed a strong correlation betweenTcf4andcollagen 3, as well as between the expression of these genes and tumor infiltration by T lymphocytes and neutrophils, attesting the clinical relevance of our findings. This study highlights the key structural role of macrophages on the tumor extracellular matrix and identifies collagen network topographies as a major regulator of tumor infiltration by immune cells.
Future heatwave conditions inhibit CO2-induced stomatal closure in wheat
Authors: Caine Robert S. , Khan Muhammad S. , Shan Yixiang , Osborne Colin P. , Croft Holly L.
Published: January 2025

Rising atmospheric CO2concentrations are driving ongoing climatic changes, leading to agricultural crops increasingly experiencing extreme weather events1. Stomata serve as gatekeepers on plant leaves, regulating both CO2capture for photosynthesis and the concomitant release of water. At higher CO2concentrations or higher vapour pressure deficit (VPD), stomatal pores narrow, reducing stomatal conductance to water vapour (gsw) and transpiration (E)2–6. Increasing temperatures and/or nitrogen fertilisation promote an opposite stomatal response, enhancinggswandE7,8. With atmospheric CO2concentration, temperature and VPD predicted to rise throughout this century1, it is unclear how crops will modify stomatal gaseous exchanges, particularly under differing N-fertilisation regimes. Here, we show in wheat (Triticum aestivum), that elevated CO2does not reducegsworEduring heatwaves when VPD is high, instead plant water usage increases. High-VPD heatwave events also impact stomatal responsiveness to N-fertiliser application, prompting significantly higher gas exchange contributions from abaxial leaf surfaces, irrespective of CO2growth conditions. Dynamic stomatal responsiveness to light and high CO2are also attenuated during heatwaves in a CO2-independent manner. Taken together, our data suggests that future wheat crops will use significantly more water during heatwaves than might be expected, which has substantial implications for future global food security.
Preserved suppressive function despite loss of Foxp3: insights into the identity of regulatory T cells
Authors: Luckerbauer B , Villarino AV , Laurence A , Hirahara K , Sciume G , Mikami Y , Shih HY , Sun HW , Tosevska A , Brinkmann M , Brooks SR , Scheffel J , Meylan F , Afzali B , Bonelli M
Published: January 2025

Regulatory T (Treg) cells are essential for maintaining immune homeostasis, with Foxp3 acting as the master transcription factor governing their differentiation and function. The acquisition of effector signatures in Treg cells is closely tied to the surrounding tissue-specific immune environment and typically occurs alongside Foxp3 expression. In this study, we investigated the transcriptomic and functional consequences of Treg-mediated regulation in a Th2-driven disease setting. The application of bothin vitrosystems andin vivodisease models allowed us to mimic Th2-mediated environments.

We could demonstrate Th2-driven loss of Foxp3 expression in Treg cellsin vitroandin vivo. Transcriptomic analysis revealed a maintained Treg signature despite the loss of active Foxp3 expression. Functional characterization of Tregs bothin vitroandin vivouncovered a preserved suppressive capacity even in the absence of Foxp3.

Our findings unveil that, despite loss of Foxp3, a preserved Treg signature remains intact enabling the regulation of Th2-mediated diseases. The persistence of this regulatory transcriptome highlights the importance for developing Treg-cell therapy strategies in cancer and autoimmune diseases independent of Foxp3 expression.
Voluntary Running Sustains the Correction of Inflammation-Related Gene Expression Conferred by AAV Gene Therapy in Mdx Mice
Authors: Yuan Claire , Hamm Shelby E. , Mack David L. , Dupont Jean-Baptiste , Grange Robert W.
Published: January 2025

Duchenne Muscular Dystrophy is a fatal disease characterized by persistent skeletal muscle degeneration, inflammation, and fibrosis. Gene therapy using an adeno-associated virus derived vector and a microdystrophin transgene is currently under investigation in patients but the impact of physical activity on long-term therapeutic outcome remains poorly understood. Recently, we reported 21-weeks of voluntary wheel running complemented the positive endurance and muscle function outcomes of gene therapy in mdx mice. In the present study, we performed a transcriptomic analysis of the gene expression changes associated with functional recovery in the diaphragm. RNA-Sequencing and bioinformatic analysis revealed 2881 dysregulated genes in untreated and unexercised mdx mice including inflammatory and fibrotic signaling pathways frequently affected in Duchenne Muscular Dystrophy patients. Among the dysregulated genes, 774 were rescued towards WT after adeno-associated virus microdystrophin injection. Importantly, 93% of the rescued genes were maintained by voluntary running, which indicates that physical exercise has no significant impact on the outcome of gene therapy in the mdx diaphragm. Our study provides vital information that could help guide DMD patient follow-up protocols after treatment with gene therapy.
Super-omics and PCAS reveal rheumatoid arthritis as a tumor-like disease
Authors: Xiao Lanlan , Aishan Nadire , Ju Siwei , Zhao Fengchao , Ouyang Xiaoxi , Chen Dazhi , Chen Weiqian , Xie Jie , Zhu Danhua , Zhang Junchi , Sun Lingyun , Li Yimin , Zhou Dan , Hu Qingqing , Wu Jinzhi , Meng Qingna , Zhou Jichun , Xu Danyi , Yu Jingyi , Liang Junyu , Cai Yangjun , Zhang Minmin , He Yanlin , Sun Zeyu , Wang Linbo , Lin Jin , Ji Feiyang
Published: January 2025

Rheumatoid arthritis (RA) is a debilitating systemic autoimmune disorder that significantly impairs quality of life. To elucidate the molecular alterations in RA progression, we performed comprehensive super-omics analyses on synovial tissues from patients with joint trauma, arthritis, and RA. These analyses included transcriptomics, proteomics, metabolomics, microbiomics, and fourteen PTMs (phosphorylation, acetylation, lactylation, O-GlcNAc glycosylation, arginine monomethylation, lysine monomethylation, lysine dimethylation, lysine trimethylation, succinylation, malonylation, glutarylation, tyrosine nitration, N-glycosylation, and O-glycosylation). Additionally, we developed a protein-centered association study (PCAS) method to integrate these complex datasets. Using this approach, we identified key proteins, such as STK17B, and its interactors, which may be crucial in RA pathogenesis. Tumor-like features, including aberrant angiogenesis and epithelial-mesenchymal transition, were observed in RA, alongside the potential involvement of oncogenes and tumor suppressor genes. Finally, we constructed a molecular interaction blueprint of RA, providing a comprehensive framework for advancing RA pathogenesis, diagnosis, and therapy.
Functional effects of deforestation on stream ecosystems in Madagascar based on growth and production of mayflies (Ephemeroptera)
Authors: Oliarinony Ranalison , Sartori Michel
Published: January 2025

The effects of deforestation on species richness and abundance of tropical freshwater organisms are increasingly well documented, but corresponding effects on functional properties of ecosystems, such as productivity and growth, are largely unknown. Here we investigated the biomass production and growth of eight species of mayflies (Ephemeroptera) in streams of eastern Madagascar. We compared three study sites in primary tropical forest with three in degraded open canopy area (savoka). All species were asynchronous and aseasonal. Seven species were multivoltine (3-4 generations per year) and one was semi-voltine. Biomass production of the most abundant species was 4-5 times greater insavokathan in forest, and standing biomass: productivity (P/B) was always higher insavoka. This production shift was mainly caused by the twoXyrodromeusspecies, both of which feed on periphytic algae that are more abundant in an open canopy. Surprisingly,Xyrodromeusfemales emerged more rapidly and were larger in size insavokathan in forest. Our results clearly indicate that deforestation in tropical Madagascar leads not only to a shift in mayfly community composition, but perhaps more importantly to functional changes in the ecosystem, namely standing biomass, annual production, and female size at maturity.
Interrupting T cell memory ameliorates exaggerated metabolic response to weight cycling
Authors: Garcia Jamie N. , Cottam Matthew A. , Rodriguez Alec S. , Hussein Agha Anwar F. , Winn Nathan C. , Hasty Alyssa H.
Published: January 2025

People frequently experience cycles of weight gain and loss. This weight cycling has been demonstrated, in humans and animal models, to increase cardiometabolic disease and disrupt glucose homeostasis. Obesity itself — and to an even greater extent weight regain — causes adipose tissue inflammation, resulting in metabolic dysfunction. Studies show that even after weight loss, increased numbers of lipid associated macrophages and memory T cells persist in adipose tissue and become more inflammatory upon weight regain. These findings suggest that the immune system retains a "memory" of obesity, which may contribute to the elevated inflammation and metabolic dysfunction associated with weight cycling. Here, we show that blocking the CD70-CD27 axis, critical for formation of immunological memory, decreases the number of memory T cells and reduces T cell clonality within adipose tissue after weight loss and weight cycling. Furthermore, while mice with impaired ability to create obesogenic immune memory have similar metabolic responses as wildtype mice to stable obesity, they are protected from the worsened glucose tolerance associated with weight cycling. Our data are the first to target metabolic consequences of weight cycling through an immunomodulatory mechanism. Thus, we propose a new avenue of therapeutic intervention by which targeting memory T cells can be leveraged to minimize the adverse consequences of weight cycling. These findings are particularly timely given the increasing use of efficacious weight loss drugs, which will likely lead to more instances of human weight cycling.
No effect of education on Telomere Length: a natural experiment in aging individuals
Authors: Judd Nicholas , Kievit Rogier
Published: January 2025

Telomere length is increasingly used as a proxy for an ‘aging exposome’ – an index of non-genetic environmental (and behavioral) exposures that an individual encounters, leading to differences in rates of aging. One of the largest associations with telomere length is schooling, leading to the suggestion of long-lasting protective effects of (additional) education. However, for ethical and practical reasons, education cannot generally be randomized, precluding an understanding of the causal effect of education on health outcomes. Here, we leverage a well-established policy change in the UK to test whether an additional year of education caused differences in telomere length decades later. Employing a fuzzy regression discontinuity design, we find no effect of education on telomere length in the UK BioBank across multiple analytic frameworks (continuity, local randomization & Bayesian approaches) and a series of robustness tests, such as increasing the analysis window around the cutoff, and changing the prior, similarly find no effect of an additional year of education on telomere length. This robust finding contrasts the prevailing ‘aging exposome account’ of telomere length and offers a cautionary note in attributing causal power to environmental factors based on observational differences.
Epigenetic mechanisms regulating CD8+ T cell senescence in aging humans
Authors: Turano Paolo S. , Akbulut Elizabeth , Dewald Hannah K. , Vasilopoulos Themistoklis , Fitzgerald-Bocarsly Patricia , Herbig Utz , Martínez-Zamudio Ricardo Iván
Published: January 2025

Aging leads to the decline of immunity, rendering the elderly susceptible to infection and disease. In the CD8+ T cell compartment, aging leads to a substantial increase of cells with high levels of senescence-associated ß-galactosidase activity (SA-ßGal) and other senescence characteristics, including a pro-inflammatory transcriptome and impaired proliferative potential. Using senescent cell isolation coupled with multiomic profiling, here we characterized the epigenetic mechanisms regulating CD8+ T cell senescence in a cohort of younger and older donors. High levels of SA-ßGal activity defined changes to global transcriptomes and chromatin accessibility landscapes, with a minor effect of age. Widespread enhancer remodeling was required for the repression of functional CD8+ T cell genes and upregulation of inflammatory and secretory pathway genes. Mechanistically, the senescence program in CD8+ T cells was controlled by chromatin state-specific transcription factor (TF) networks whose composition was largely insensitive to donor age. Pharmacological inhibition of TF network nodes AP1, KLF5, and RUNX2 modulated the transcriptional output, demonstrating the feasibility of TF network perturbation as an approach to modulate CD8+ T cell senescence. Further, CD8+ T cell senescence gene signatures faithfully predicted refractoriness to chimeric antigen receptor (CAR) T-cell therapy in a cohort of diffuse large B cell lymphomas and were highly enriched in the transcriptomes of peripheral CD8+ T cells of individuals with active systemic lupus erythematosus. Collectively, our findings demonstrate the potential of multiomic profiling in identifying key regulators of senescence across cell types and suggest a critical role of senescent CD8+ T cells in disease progression.
Mammal niches are not conserved over continental scales
Authors: Goldstein Benjamin R. , Pacifici Krishna , Jensen Alex J. , Reich Brian J. , Cove Michael V. , McShea William J. , Rooney Brigit , Kierepka Elizabeth M. , Roberts Rachel A. , Kays Roland
Published: January 2025

Summary paragraph

The niche conservatism hypothesis states that a species’ relationships to habitat and climate conditions are maintained across space and time1–6. Niche stationarity is assumed when ecologists estimate species’ habitat needs or transfer findings across geographic regions7,8. Recent studies show that some species’ associations with climate and habitat vary spatially, contradicting the niche conservatism hypothesis9–18. The sources of this nonstationarity are unknown and potential mechanisms remain untested. Here we show that the environmental niches of 36 common North American mammals vary spatially across dimensions of human influence, climate, and landscape. Spatial variation is not explained by known genetic subspecies lineages. Instead, niches vary at a relatively fine spatial scale consistent with adaptations by animals to local conditions, which may be explained by genetic or behavioral changes or by unmodeled interactions with unobserved variables. Spatially varying ecology means that static niche models are not appropriate at large scales and extrapolating species’ niches to novel contexts may be impossible19. This complicates management decisions based on transferring findings across space and projecting species’ current environmental associations to responses to future change, but may provide optimism if nonstationarity represents potential for rapid evolutionary rescue.
First occurrence of Ranavirus in Scandinavian peninsula
Authors: Thumsová B , Chondrelli N , Valdés AE , Eghbal R , Höglund J , Laurila A , Bosch J , Cortázar-Chinarro M
Published: January 2025

Emerging infectious diseases (EIDs) pose a major threat to global amphibian populations, contributing to widespread mortality and species extinctions. Among EIDs, those caused by fungal infection pathogensBatrachochytrium dendrobatidis(Bd) andB. salamandrivorans(Bsal), and viral infections of the genus Ranavirus (Rv), represent the most significant threats to amphibian biodiversity. Here, we test for occurrence ofRvinfection in three different locations in southeastern Sweden. Using a quantitative PCR (qPCR) assay, complemented by a secondary PCR-based validation method targeting the viral major capsid protein gene (MCP) and additional five partial sequences, we detectedRvinfection in two of three locations and in five out of 43 individuals tested. This is the first confirmed record ofRvoccurrence reported at such high latitudes in north Europe and the first one from Scandinavian peninsula, contributing important insights into infection prevalence in northern amphibian populations. These findings establish a basis for further research for the conservation of these vulnerable populations.
Markovian State Models uncover Casein Kinase 1 dynamics that govern circadian period
Authors: Ricci Clarisse Gravina , Philpott Jonathan M. , Torgrimson Megan R. , Freeberg Alfred M. , Narasimamurthy Rajesh , Pécora de Barros Emilia , Amaro Rommie , Virshup David M. , McCammon J. Andrew , Partch Carrie L.
Published: January 2025

Circadian rhythms in mammals are tightly regulated through phosphorylation of Period (PER) proteins by Casein Kinase 1 (CK1, subtypes δ and ε). CK1 acts on at least two different regions of PER with opposing effects: phosphorylation of phosphodegron (pD) regions leads to PER degradation, while phosphorylation of the Familial Advanced Sleep Phase (FASP) region leads to PER stabilization. To investigate how substrate selectivity is encoded by the conformational dynamics of CK1, we performed a large set of independent molecular dynamics (MD) simulations of wildtype CK1 and thetaumutant (R178C) that biases kinase activity toward a pD. We used Markovian State Models (MSMs) to integrate the simulations into a single model of the conformational landscape of CK1 and used Gaussian accelerated molecular dynamics (GaMD) to build the first molecular model of CK1 and the unphosphorylated FASP motif. Together, these findings provide a mechanistic view of CK1, establishing how the activation loop acts as a key molecular switch to control substrate selectivity. We show that thetaumutant favors an alternative conformation of the activation loop and significantly accelerates the dynamics of CK1. This reshapes the binding cleft in a way that impairs FASP binding and would ultimately lead to PER destabilization and shorter circadian periods. Finally, we identified an allosteric pocket that could be targeted to bias this molecular switch. Our integrated approach offers a detailed model of CK1’s conformational landscape and its relevance to normal, mutant, and druggable circadian timekeeping.

Statement of Significance

Disruption of circadian rhythms alters the temporal orchestration of vital cellular processes and increases the propensity for sleep disorders, metabolic disease, and cancer. Circadian rhythms are generated by a vast gene expression program controlled at the cellular level by a molecular clock comprised of dedicated clock proteins. Amongst the essential protein characters is Casein kinase 1 (CK1), which acts on multiple clock protein substrates. A delicate balance of CK1 activity on these substrates is crucial for proper circadian timekeeping, highlighting CK1 as a promising drug target to tune clock timing. This work aims to identify the conformational landscape of CK1 that underlies its substrate specificity and provide molecular insight for pharmacologic development that could modulate CK1 function for those suffering from clock-related syndromes.
Hydrodynamic Circulation, Ecological Drift, and Homogeneous Selection Shape Microbial Communities and Biogeochemical Cycling in Lake Ontario
Authors: Pendleton Augustus , Schmidt Marian L.
Published: January 2025

Microbial communities are vital to the ecology of the Laurentian Great Lakes, yet the influence of point sources, community assembly processes, and hydrodynamic circulation on their abundance and structure remains poorly understood. To address this, we analyzed 16S rDNA gene sequencing, flow cytometry, and water quality data from Lake Ontario during May and September of 2023. Communities were grouped into three depth-month categories: Shallow May, Shallow September, and Deep. Deep communities were dominated by drift, with some dispersal limitation, while shallow communities were shaped by homogenizing selection, especially in September, with contributions from drift. Actinobacteria were associated with homogenizing selection, Alphaproteobacteria with drift, and Bacteroidia in May and Chloroflexi in September with dispersal limitation. Upwellings altered microbial abundance and composition, modifying nitrogen cycling gene abundance. These findings provide insights into the ecological implications for Great Lakes health and conservation, emphasizing how upwelling events create unique microbial communities within the lake.
Female fibroblast activation is estrogen-mediated in sex-specific 3D-bioprinted pulmonary artery adventitia models
Authors: Mueller Mikala C. , Blomberg Rachel , Tanneberger Alicia E. , Davis-Hall Duncan , Neeves Keith B. , Magin Chelsea M.
Published: January 2025

Pulmonary arterial hypertension (PAH) impacts male and female patients in different ways. Female patients exhibit a greater susceptibility to disease (4:1 female-to-male ratio) but live longer after diagnosis than male patients. This complex sexual dimorphism is known as the estrogen paradox. Prior studies suggest that estrogen signaling may be pathologic in the pulmonary vasculature and protective in the heart, yet the mechanisms underlying these sex-differences in PAH remain unclear. PAH is a form of a pulmonary vascular disease that results in scarring of the small blood vessels, leading to impaired blood flow and increased blood pressure. Over time, this increase in blood pressure causes damage to the heart. Many previous studies of PAH relied on male cells or cells of undisclosed origin forin vitromodeling. Here we present a dynamic, 3D-bioprinted model that incorporates cells and circulating sex hormones from female patients to specifically study how female patients respond to changes in microenvironmental stiffness and sex hormone signaling. Poly(ethylene glycol)-alpha methacrylate (PEGαMA)-based hydrogels containing female human pulmonary artery adventitia fibroblasts (hPAAFs) from idiopathic PAH (IPAH) or control donors were 3D bioprinted to mimic pulmonary artery adventitia. These biomaterials were initially soft, like healthy blood vessels, and then stiffened using light to mimic vessel scarring in PAH. These 3D-bioprinted models showed that stiffening the microenvironment around female IPAH hPAAFs led to hPAAF activation. On both the protein and gene-expression levels, cellular activation markers significantly increased in stiffened samples and were highest in IPAH patient-derived cells. Treatment with a selective estrogen receptor modulator reduced expression hPAAF activation markers, demonstrating that hPAAF activation is a one pathologic response mediated by estrogen signaling in the vasculature, validating that drugs currently in clinical trials could be evaluated in sex-specific 3D-bioprinted pulmonary artery adventitia models.
Neoplastic immune mimicry potentiates breast tumor progression
Authors: Berens Eric B. , Khou Sokchea , Huang Elaine , Hoffman Amber , Johnson Briana , Kirchberger Nell , Sivagnanam Shamilene , Calistri Nicholas L. , Derrick Daniel , Liby Tiera A. , McLean Ian C. , Alanizi Aryn A. , Ozmen Furkan , Ozmen Tugba Y. , Mills Gordon B. , Hwang E. Shelley , Schedin Pepper J. , Gonzalez Hugo , Werb Zena , Heiser Laura M. , Coussens Lisa M.
Published: January 2025

Dedifferentiation programs are commonly enacted during breast cancer progression to enhance tumor cell fitness. Increased cellular plasticity within the neoplastic compartment of tumors correlates with disease aggressiveness, often culminating in greater resistance to cytotoxic therapies or augmented metastatic potential. Here we report that subpopulations of dedifferentiated neoplastic breast epithelial cells express canonical leukocyte cell surface receptor proteins and have thus named this cellular program “immune mimicry.” We document neoplastic cells engaging in immune mimicry within public human breast tumor single-cell RNA-seq datasets, histopathological breast tumor specimens, breast cancer cell lines, as well as in murine transgenic and cell line-derived mammary cancer models. Immune-mimicked neoplastic cells harbor hallmarks of dedifferentiation and are enriched in treatment-resistant and high-grade breast tumors. We corroborated these observations in aggressive breast cancer cell lines where anti-proliferative cytotoxic chemotherapies drove epithelial cells toward immune mimicry. Moreover, in subsequent proof-of-concept studies, we demonstrate that expression of the CD69 leukocyte activation protein by neoplastic cells confers a proliferative advantage that facilitates early tumor growth and therefore conclude that neoplastic breast epithelial cells upregulating leukocyte surface receptors potentiate malignancy. Moving forward, neoplastic immune mimicry should be evaluated for prognostic utility in breast cancer to determine stratification potential for patients with increased risks of tumor recurrence, metastasis, and therapeutic resistance.

One Sentence Summary

Neoplastic breast epithelial cells express surface receptors canonically attributed to leukocytes and are associated with therapy resistance and aggressive tumor behavior.
Identification of regions required for allelic specificity at the cell wall remodeling allorecognition checkpoint inNeurospora crassa
Authors: Rico-Ramirez Adriana M. , Glass N. Louise
Published: January 2025

Allorecognition is the ability of organisms/cells to differentiate self from non-self. In the fungusNeurospora crassa, allorecognition systems serve as checkpoints to restrict germling/hyphal fusion between genetically incompatible strains. Thecellwallremodeling (cwr) checkpoint functions after chemotrophic interactions and is triggered upon cell/hyphal contact, regulating cell wall dissolution and subsequent cell fusion. Thecwrregion consists of two linked loci,cwr-1andcwr-2, that are under severe linkage disequilibrium. Phylogenetic analysis of wildN. crassapopulations showed thatcwr-1/cwr-2alleles fall into six different haplogroups (HGs). Strains containing deletions ofcwr-1andcwr-2will fuse with previously HG incompatible cells, indicatingcwrnegatively regulates cell fusion. CWR-1 encodes a polysaccharide monooxygenase (PMO) domain that oxidatively degrades chitin; the PMO domain is sufficient to cause fusion arrest and confers allelic specificity by interactingin transwith CWR-2, a predicted transmembrane protein. However, the catalytic activity of CWR-1 is not required for triggering a block in cell fusion. The L2 and LC regions of the CWR-1 PMO domain show high levels of structural variability between different HGs. CWR-1 chimeras containing a LC region from a different HG were sufficient to trigger a cell fusion block, but not quite at wild type levels, suggesting that the complete PMO structure is necessary for allorecognition. Modeling of the transmembrane protein CWR-2 revealed allelic variability in the two major extracellular domains (ED2/ED4). Chimeras of CWR-2 with swapped ED2 or ED4 or ED2/ED4 domains from differentcwr-2haplogroups also altered allelic specificity.

Allorecognition or nonself recognition enables fungi to distinguish genetically different individuals, thereby regulating cooperation to form mycelial networks. This study focused on the cell wall remodeling checkpoint (cwr), where genetic differences in two genes,cwr-1andcwr-2, triggers allorecognition. Upon cell contact, CWR-1 in one cell functionsin transwith CWR-2 in a second cell to confer a block in cell fusion. Chimeric proteins were created and tested to pinpoint domains involved in allelic specificity. For CWR-1, the L2 and LC domains are critical, while for CWR-2, the ED2 and ED4 domains have an important role in regulating cell fusion.Graphical Abstract
Enantioselective Protein Affinity Selection Mass Spectrometry (EAS-MS)
Authors: Wang Xiaoyun , Sun Jianxian , Ahmad Shabbir , Yang Diwen , Li Fengling , Chan U Hang , Zeng Hong , Simoben Conrad V. , Houliston Scott , Dong Aiping , Bolotokova Albina , Gibson Elisa , Kutera Maria , Ghiabi Pegah , Kondratov Ivan , Matviyuk Tetiana , Chuprina Alexander , Mavridi Danai , Lenz Christopher , Joerger Andreas C. , Brown Benjamin D. , Heath Richard B. , Yue Wyatt W. , Robbie Lucy K. , Beyett Tyler S. , Müller Susanne , Knapp Stefan , Harding Rachel , Schapira Matthieu , Brown Peter J. , Santhakumar Vijayaratnam , Ackloo Suzanne , Arrowsmith Cheryl H. , Edwards Aled M. , Peng Hui , Halabelian Levon
Published: January 2025

We report an enantioselective protein affinity selection mass spectrometry screening approach (EAS-MS) that enables the detection of weak binders, informs about selectivity, and generates orthogonal confirmation of binding. After method development with control proteins, we screened 31 human proteins against a designed library of 8,210 chiral compounds. 16 binders to 12 targets, including many proteins predicted to be “challenging to ligand”, were discovered and confirmed in orthogonal assays. 7 binders to 6 targets bound in an enantioselective manner, withKDs ranging from 3 to 20 µM. Binders for four targets (DDB1, WDR91, WDR55, and HAT1) were selected for in-depth characterization using X-ray crystallography. In all four cases, the mechanism for enantioselective selectivity was readily explained. EAS-MS can be used to identify and characterize selective and weakly-binding ligands for novel protein targets with unprecedented throughput and sensitivity.