bluuebunny/crossref_metadata_2025 huggingface dataset:
Activation of the p62‐Keap1‐Nrf2 pathway improves pulmonary arterial hypertension in MCT‐induced rats by inhibiting autophagy
Authors: Jiang Gang , Shi Li‐Fang , Li Ling‐Jiao , Duan Xiao‐Ju , Zheng Zhao‐Fen
Published: February 2024

Autophagy is implicated in the pathogenesis of pulmonary arterial hypertension (PAH). We aimed to investigate whether the p62‐Keap1‐Nrf2 pathway affects the development of PAH by mediating autophagy. A PAH rat model was established using monocrotaline (MCT). Pulmonary artery smooth muscle cells (PASMCs) were extracted, and the changes in proliferation, migration, autophagy, and oxidative stress were analyzed following overexpression or knockdown of p62. The impact of p62 on the symptoms of PAH rats was assessed by the injection of an adenovirus overexpressing p62. We found that the knockdown of p62 increased the proliferation and migration of PASMCs, elevating the oxidative stress of PASMCs and upregulating gene expression of NADPH oxidases. Co‐IP assay results demonstrated that p62 interacted with Keap1. p62 knockdown enhanced Keap1 protein stability and Nrf2 ubiquitination. LC3II/I and ATG5 were expressed more often when p62 was knocked down. Treating with an inhibitor of autophagy reversed the impact of p62 knockdown on PASMCs. Nrf2 inhibitor treatment reduced the expression of Nrf2 and p62, while increasing the expression of Keap1, LC3II/I, and ATG5 in PASMCs. However, overexpressing p62 diminished mRVP, SPAP, and Fulton index in PAH rats and attenuated pulmonary vascular wall thickening. Overexpression of p62 also decreased the expression of Keap1, LC3II/I, and ATG5 and increased the nuclear expression of Nrf2 in PAH rats. Importantly, overexpression of p62 reduced oxidative stress and the NADPH oxidase expression in PAH rats. Overall, activation of the p62‐Keap1‐Nrf2 positive feedback signaling axis reduces the proliferation and migration of PASMCs and alleviates PAH by inhibiting autophagy and oxidative stress.
Ruxolitinib, IV Immunoglobulin, and High-Dose Glucocorticoids for Critically Ill Adults With Secondary Hemophagocytic Lymphohistiocytosis: A Single-Center Observational Pilot Study
Authors: Scholz Laura , Posch Florian , Schulz Eduard , Gornicec Max , Wölfler Albert , Reisinger Alexander C. , Reinisch Andreas , Eller Philipp , Eisner Florian , Kreuzer Philipp , Stradner Martin , Rosenkranz Alexander R. , Krammer Florian , Schilcher Gernot , Krause Robert , Hatzl Stefan
Published: February 2024

OBJECTIVES:

Secondary hemophagocytic lymphohistiocytosis (sHLH) is a cytokine-driven inflammatory syndrome that is associated with substantial morbidity and mortality and frequently leads to ICU admission. Overall survival in adults with sHLH remains poor, especially in those requiring intensive care. Classical chemotherapeutic treatment exhibits myelosuppression and toxicity. Recently, inhibition of Janus kinase signaling by ruxolitinib has shown efficacy in pediatric HLH. We therefore aimed to determine the activity and safety of a ruxolitinib-based regimen, in critically ill adults with sHLH.

DESIGN:

Observational pilot study.

SETTING:

Single-center tertiary academic ICU.

PATIENTS:

Nine adults (≥ 18 yr) who fulfilled at least five of the eight HLH-2004 criteria.

INTERVENTION:

Triplet regimen combining: 1) ruxolitinib, 2) polyvalent human IV immunoglobulins (IVIG) at a dose of 1 g/kg bodyweight for 5 days, and 3) high-dose corticosteroids (CSs, dexamethasone 10 mg/m² body surface area, or methylprednisolone equivalent) with subsequent tapering according to the HLH-2004 protocol.

MEASUREMENT AND MAIN RESULTS:

Nine patients (median age: 42 yr [25th-75th percentile: 32–54]; male: n = 6 males, median H-score: 299 [255–304]) were treated with the triplet regimen. The median Sequential Organ Failure Assessment score at HLH diagnosis was 9 (median; 25th–75th percentile: 7–12), indicating multiple-organ dysfunction in all patients. Within 10 days a significant decrease of the inflammatory parameters soluble interleukin-2 receptor and ferritin as well as a stabilization of the blood count could be shown. All patients were alive at ICU discharge (100% ICU survival), 1 patient died after ICU discharge because of traumatic intracerebral hemorrhage that might be related to HLH or treatment, corresponding to an overall survival of 86% in a 6 months follow-up period.

CONCLUSION:

In this small case series, a triplet regimen of ruxolitinib in combination with IVIG and CS was highly effective and save for treating critically ill adults with sHLH.
Atypical perforated appendicitis secondary to schistosomiasis: a rare case report
Authors: Osoble Osman Faisal Abdi , Mohamed Yahye Garad , Salad Najib Mohamed , Yahye Nuh Mohamed
Published: February 2024

Introduction:

Schistosomiasis is the second most common parasite disease after malaria and a rare cause of appendicitis. It has been well-documented in the literature that schistosomiasis infection can have several multisystem effects. The unusual condition known as schistosomal appendicitis was initially described by Turner.

Case presentation:

We present a 48-year-old man with perforated appendicitis and schistosomiasis-like radiological findings. An appendectomy was performed, and schistosomiasis was confirmed by a histological study of the excised appendix. Praziquantel was administered in a single dosage.

Conclusion:

Although schistosomiasis is a rare cause of appendicitis and is very prevalent in developing nations, it should be considered when managing the condition. Anti-shistosoma drugs, which are not frequently used in post-appendectomy cases, should also be considered in the management.
Comparison of the effect of open-box versus closed-box prostheses on blood loss following total knee arthroplasty: a meta-analysis
Authors: Elhalag Rowan H. , Dean Yomna E. , Hamdy Anas , Hadhoud Abdalla Mohamed , Chébl Pensée , Shah Jaffer , Gawad Mohamed , Motawea Karam R.
Published: February 2024

Purpose:

Postoperative blood loss is a common complication following total knee arthroplasty (TKA). The authors aimed to analyze the significance of open versus closed-box prostheses in reducing blood loss after TKA.

Methods:

PubMed, Cochrane, Scopus, and Web of Science were searched. Observational studies and clinical trials comparing the effect of open-box versus closed-box prostheses on blood loss following TKA were included. The primary outcome was total blood loss following TKA. Secondary outcomes included average transfused units and total operation time. Continuous data were represented as mean difference (MD) and CI, while dichotomous data were presented as odds ratio (OR) and CI. RevMan software version 5.4 was used to conduct the analysis.

Results:

Four studies with a total number of 687 patients were included. The pooled analysis showed a statistically significant association between closed-box and decreased total blood loss following TKA compared with open-box (MD=173.19, 95% CI=88.77–257.61, P value <0.0001). Similar findings were reported in unilateral TKA (MD=190.63, 95% CI=70.91–310.35, P value=0.002), and bilateral TKA (MD=160.79, 95% CI=61.70–359.86, P value=0.001). There was no significant difference between open and closed-box regarding average transfused units (MD=0.02, 95% CI=−0.07–0.11, P value=0.68), blood transfusion rate (OR=1.38, 95% CI=0.85–2.26, P value=0.20), length of stay (MD=0.06, 95% CI=−0.27 to 0.38, P value=0.74), and total operation time (MD=1.08, 95% CI=−4.62 to 6.79, P value=0.71).

Conclusion:

Closed-box reduces the total blood loss following unilateral and bilateral TKA. More studies are warranted to explore the benefits of Closed-box in patients with high bleeding susceptibility.
Dissecting reprogramming heterogeneity at single-cell resolution using scTF-seq
Authors: Liu Wangjie , Saelens Wouter , Rainer Pernille , Biočanin Marjan , Gardeux Vincent , Gralak Antoni , van Mierlo Guido , Russeil Julie , Liu Tingdang , Chen Wanze , Deplancke Bart
Published: February 2024

Reprogramming approaches often produce heterogeneous cell fates and the mechanisms behind this heterogeneity are not well-understood. To address this gap, we developed scTF-seq, a technique inducing single-cell barcoded and doxycycline-inducible TF overexpression while quantifying TF dose-dependent transcriptomic changes. Applied to mouse embryonic multipotent stromal cells (MSCs), scTF-seq produced a gain-of-function atlas for 384 murine TFs. This atlas offers a valuable resource for gene regulation and reprogramming research, identifying key TFs governing MSC lineage differentiation, cell cycle control, and their interplay. Leveraging the single-cell resolution, we dissected reprogramming heterogeneity along dose and pseudotime. We thereby revealed TF dose-dependent and stochastic cell fate branching, unveiling gene expression signatures that enhance our understanding and prediction of reprogramming efficiency. scTF-seq also allowed us to classify TFs into four sensitivity classes based on dose response and determining features. Finally, in combinatorial scTF-seq, we observed that the same TF can exhibit both synergistic and antagonistic effects on another TF depending on its dose. In summary, scTF-seq provides a powerful tool for gaining mechanistic insights into how TFs determine cell states, while offering novel perspectives for cellular engineering strategies.
TBX3 is essential to establish the posterior boundary of anterior genes and up-regulate posterior genes with HAND2 during onset of limb bud development
Authors: Soussi Geoffrey , Girdziusaite Ausra , Jhanwar Shalu , Palacio Victorio , Sheth Rushikesh , Zeller Rolf , Zuniga Aimée
Published: February 2024

During limb bud formation, axes polarities are established as evidenced by the spatially restricted expression of key regulator genes. In particular, the mutually antagonistic interaction between the GLI3 repressor and HAND2 results in the distinct and non-overlapping anterior-distalGli3and posteriorHand2expression domains. This hallmarks establishment of antero-posterior (AP) limb axis polarity together with spatially restricted expression of homeodomain and other transcriptional regulators. Here, we identify TBX3 as the transcription factor to initiate AP axis polarity in mouse limb buds. ChIP-seq and differential gene expression analysis of wildtype and mutant limb buds identifies the TBX3-specific and shared TBX3-HAND2 target genes. High sensitivity fluorescent whole mountin situhybridisation shows that the posterior expression boundaries of anterior genes are positioned by TBX3-mediated repression, which excludes anterior genes such asGli3,Alx4,Hand1andIrx3/5from the posterior limb bud mesenchyme. This exclusion delineates the posterior mesenchymal territory competent to establish theShh-expressing limb bud organiser. In turn, HAND2 is required forShhactivation and cooperates with TBX3 to up-regulate shared posterior identity target genes in early limb buds.
Meta-analyses of mouse and human prostate single-cell transcriptomes reveal widespread epithelial plasticity in tissue regression, regeneration, and cancer
Authors: Aparicio Luis , Crowley Laura , Christin John R. , Laplaca Caroline J. , Hibshoosh Hanina , Rabadan Raul , Shen Michael M.
Published: February 2024

Recent advances in single-cell RNA-sequencing (scRNA-seq) technology have facilitated studies of cell states and plasticity in tissue maintenance and cancer, including in the prostate. Here we present meta-analyses of multiple new and published scRNA-seq datasets to establish reference cell type classifications for the normal mouse and human prostate. Our analyses demonstrate transcriptomic similarities between epithelial cell states in the normal prostate, in the regressed prostate after androgen-deprivation, and in primary prostate tumors. During regression in the mouse prostate, all epithelial cells shift their expression profiles towards a proximal periurethral (PrU) state, demonstrating an androgen-dependent plasticity that is restored to normal during androgen restoration and regeneration. In the human prostate, we find progressive rewiring of transcriptional programs across epithelial cell types in benign prostate hyperplasia and treatment-naïve prostate cancer. Notably, we detect copy number variants predominantly within Luminal Acinar cells in prostate tumors, suggesting a bias in their cell type of origin, as well as a larger field of transcriptomic alterations in non-tumor cells. Finally, we observe that Luminal Acinar tumor cells in treatment-naïve prostate cancer display heterogeneous androgen receptor (AR) signaling activity, including a split between high-AR and low-AR profiles with similarity to PrU-like states. Taken together, our analyses of cellular heterogeneity and plasticity provide important translational insights into the origin and treatment response of prostate cancer.
Towards Equitable MHC Binding Predictions: Computational Strategies to Assess and Reduce Data Bias
Authors: Glynn Eric , Ghersi Dario , Singh Mona
Published: February 2024

Deep learning tools that predict peptide binding by major histocompatibility complex (MHC) proteins play an essential role in developing personalized cancer immunotherapies and vaccines. In order to ensure equitable health outcomes from their application, MHC binding prediction methods must work well across the vast landscape of MHC alleles. Here we show that there are alarming differences across individuals in different racial and ethnic groups in how much binding data are associated with their MHC alleles. We introduce a machine learning framework to assess the impact of this data disparity for predicting binding for any given MHC allele, and apply it to develop a state-of-the-art MHC binding prediction model that additionally provides per-allele performance estimates. We demonstrate that our MHC binding model successfully mitigates much of the data disparities observed across racial groups. To address remaining inequities, we devise an algorithmic strategy for targeted data collection. Our work lays the foundation for further development of equitable MHC binding models for use in personalized immunotherapies.
NOTCH1 fusions in pediatric T-cell lymphoblastic lymphoma: a high-risk subgroup with CCL17 (TARC) levels as diagnostic biomarker
Authors: Kroeze Emma , Kleisman Michelle M , Kester Lennart A , Scheijde-Vermeulen Marijn A , Sonneveld Edwin , Buijs-Gladdines Jessica GC , Hagleitner Melanie M , Meyer-Wentrup Friederike AG , Veening Margreet A , Beishuizen Auke , Meijerink Jules PP , Loeffen Jan LC , Kuiper Roland P
Published: February 2024

Twenty percent of children with T-cell lymphoblastic lymphoma (T-LBL) will relapse and have an extremely poor outcome. Currently, we can identify a genetically low-risk subgroup in pediatric T-LBL, yet these high-risk patients who need intensified or alternative treatment options remain undetected. Therefore, there is an urgent need to recognize these high-risk T-LBL patients through identification of molecular characteristics and biomarkers. By using RNA sequencing which was performed in 29/49 T-LBL patients who were diagnosed in the Princess Maxima Center for Pediatric Oncology between 2018-2023, we discovered a previously unknown high-risk biological subgroup of children with T-LBL. This subgroup is characterized byNOTCH1gene fusions, found in 21% of our T-LBL cohort (6/29). All patients presented with a large mediastinal mass, pleural/pericardial effusions, and absence of blasts in the bone marrow, blood, and central nervous system. Blood CCL17 (C-C Motif Chemokine Ligand 17, TARC) levels were measured at diagnosis in 26/29 patients, and all six patients withNOTCH1gene fusions patients exclusively expressed highly elevated blood CCL17 levels, defining a novel and previously not known clinically relevant biomarker for T-cell lymphoblastic lymphoma. Four out of these six patients relapsed during therapy, a fifth developed a therapy related acute myeloid leukemia during maintenance therapy. These data indicate that T-LBL patients with aNOTCH1fusion have a high risk of relapse which can be easily identified using a blood CCL17 screening at diagnosis. Further molecular characterization throughNOTCH1gene fusion analysis offers these patients the opportunity for treatment intensification or new treatment strategies.
High-throughput neural stem cell-based drug screening identifies S6K1 inhibition as a selective vulnerability in SHH-medulloblastoma
Authors: Zhou Leilei , van Bree Niek , Boutin Lola , Moussaud Simon , Otrocka Magdalena , Falk Anna , Wilhelm Margareta
Published: February 2024

Background

Medulloblastoma (MB) is one of the most common malignant brain tumors in children. Current treatments have increased overall survival but can lead to devastating side effects and late complications in survivors, emphasizing the need for new, improved targeted therapies that specifically eliminate tumor cells while sparing the normally developing brain.

Methods

Here, we used a SHH-MB model based on a patient-derived neuroepithelial stem (NES) cell system for an unbiased high-throughput screen with a library of 172 compounds with known targets. Compounds were evaluated in both healthy neural stem cells and tumor cells derived from the same patient. Based on the difference of cell viability and drug sensitivity score between normal cells and tumor cells, hit compounds were selected and further validatedin vitroandin vivo.

Results

We identified PF4708671 (S6K1 inhibitor) as a potential agent that selectively targets Sonic Hedgehog (SHH) driven MB tumor cells while sparing neural stem cells and differentiated neurons. Subsequent validation studies confirmed that PF4708671 inhibited the growth of SHH-MB tumor cells bothin vitroandin vivo, and that knockdown of S6K1 resulted in reduced tumor formation.

Conclusion

Overall, our results suggest that inhibition of S6K1 specifically affects tumor growth, whereas it has less effect on non-tumor cells. Our data also show that the NES cell platform can be used to identify potentially effective new therapies and targets for SHH-MB.

Key points

High-throughput screening system using the NES model identifies efficient compounds and targets against SHH-MB.

S6K1 inhibition shows selectivity toward tumor cells while having less effect on normal neural stem cells and neurons.

Importance of the study

Current treatment modalities for medulloblastoma have improved overall survival but also come with detrimental side effects for survivors. Therefore, novel treatment options need to be developed which will specifically target the tumor cells while sparing the healthy brain. In this study, we tested a library of compounds targeting commonly dysregulated oncogenic pathways on both normal neural stem cells and SHH-MB tumor cells derived from the same patients. Interestingly, we found that most compounds including commonly used targeted therapy such as PI3K or mTOR inhibition, albeit effective, affected tumor cells and normal cells similarly. However, inhibition of the downstream effector S6K1 preferentially targeted tumor cells bothin vitroandin vivo. These results thus reveal potential targets for translational studies of novel therapies that specifically target medulloblastoma tumor cells.
SPIRED-Fitness: an end-to-end framework for the prediction of protein structure and fitness from single sequence
Authors: Chen Yinghui , Xu Yunxin , Liu Di , Xing Yaoguang , Gong Haipeng
Published: February 2024

Abstract

Significant research progress has been made in the field of protein structure and fitness prediction. Particularly, single-sequence-based structure prediction methods like ESMFold and OmegaFold achieve a balance between inference speed and prediction accuracy, showing promise for many downstream prediction tasks. Here, we propose SPIRED, a novel single-sequence-based structure prediction model that exhibits comparable performance to the state-of-the-art methods but with approximately 5-fold acceleration in inference and at least one order of magnitude reduction in training consumption. By integrating SPIRED with downstream neural networks, we compose an end-to-end framework named SPIRED-Fitness for the rapid prediction of both protein structure and fitness from single sequence. SPIRED-Fitness and its derivative SPIRED-Stab achieve state-of-the-art performance in predicting the mutational effects on protein fitness and stability metrics, respectively.
mTORC1 Activation In Presumed Classical Monocytes: Observed Correlates With Human Size Variation and Neuropsychiatric Disease
Authors: Berner Karl , Oz Naci , Kaya Alaattin , Acharjee Animesh , Berner Jon
Published: February 2024

Background

Gain of function disturbances in nutrient sensing are likely the largest component in human age-related disease. Mammalian target of rapamycin complex 1 (mTORC1) activity affects health span and longevity. The drugs ketamine and rapamycin are effective against chronic pain and depression, and both affect mTORC1 activity. Our objective was to measure phosphorylated p70S6K, a marker for mTORC1 activity, in individuals with psychiatric disease to determine whether phosphorylated p70S6K could predict medication response.

Methods

Twenty-seven females provided blood samples in which p70S6K and phosphorylated p70S6K were analyzed. Chart review gathered biometric measurements, clinical phenotypes, and medication response. Questionnaires assessed anxiety, depression, autism traits, and mitochondrial dysfunction, to determine neuropsychiatric disease profiles. Univariate and multivariate statistical analyses were used to identify predictors of medication response.

Results

mTORC1 activity correlated highly with both classical biometrics (height, macrocephaly, pupil distance) and specific neuropsychiatric disease profiles (anxiety and autism). Across all cases, phosphorylated p70S6K was the best predictor for ketamine response, and also the best predictor for rapamycin response in a single instance.

Conclusions

The data illustrates the importance of mTORC1 activity in both observable body structure and medication response. This report suggests that a simple assay may allow cost-effective prediction of medication response.
Grb7,Grb10andGrb14,encoding the growth factor receptor-bound 7 family of signalling adaptor proteins have overlapping functions in the regulation of fetal growth and post-natal glucose metabolism
Authors: Moorwood Kim , Smith Florentia M. , Garfield Alastair S. , Cowley Michael , Holt Lowenna J. , Daly Roger J. , Ward Andrew
Published: February 2024

Background

The growth factor receptor bound 7 (Grb7) family of signalling adaptor proteins comprises Grb7, Grb10 and Grb14. Each can interact with the insulin receptor and other receptor tyrosine kinases, where Grb10 and Grb14 inhibit insulin receptor activity. In cell culture studies they mediate functions including cell survival, proliferation, and migration. Mouse knockout (KO) studies have revealed physiological roles forGrb10andGrb14in glucose-regulated energy homeostasis. BothGrb10KO andGrb14KO mice exhibit increased insulin signalling in peripheral tissues, with increased glucose and insulin sensitivity and a modestly increased ability to clear a glucose load. In addition,Grb10strongly inhibits fetal growth such that at birthGrb10KO mice are 30% larger by weight than wild type littermates.

Results

Here, we generate aGrb7KO mouse model. We show that during fetal development the expression patterns of Grb7 and Grb14 each overlap with that of Grb10. Despite this,Grb7andGrb14did not have a major role in influencing fetal growth, either alone or in combination withGrb10. At birth, in most respects bothGrb7KO andGrb14KO single mutants were indistinguishable from wild type, whileGrb7:Grb10double knockout (DKO) were near identical toGrb10KO single mutant andGrb10:Grb14DKO mutants slightly smaller. In the developing kidneyGrb7had a subtle positive influence on growth. An initial characterisation ofGrb7KO adult mice revealed sexually dimorphic effects on energy homeostasis, with females having significantly smaller white adipose tissue (WAT) depots and an enhanced ability to clear glucose from the circulation, compared to wild type littermates. Males had elevated fasted glucose levels with a trend towards smaller WAT depots, without improved glucose clearance.

Conclusions

Grb7andGrb14do not have significant roles as inhibitors of fetal growth, unlikeGrb10, and insteadGrb7may promote growth of the developing kidney. In adulthood,Grb7contributes subtly to glucose mediated energy homeostasis, raising the possibility of redundancy between all three adaptors in physiological regulation of insulin signalling and glucose handling.
Thermodynamics determines the coupling between growth and byproduct production
Authors: Oftadeh Omid , Hatzimanikatis Vassily
Published: February 2024

Genetic manipulation of cells to couple byproduct production and growth rate is important in bioengineering and biotechnology. In this way, we can use growth rate as a selective pressure, where the mutants with higher growth have higher production capacity. Computational methods have been proposed to find knockouts that couple growth and byproduct production. However, none of these methods consider the energetic and thermodynamic feasibility of such knockout strategies. Furthermore, there is no computational study of how variations in metabolite concentrations affect the coupling between growth and byproduct formation. One of the computational methods to find knockouts that couple growth and byproduct formation is OptKnock. OptKnock is a bi-level optimization problem. Here, we integrated thermodynamic constraints into the bilevel formulation of OptKnock to create TOptKnock. We show that the computational efficiency of TOptKnock is comparable to that of OptKnock. TOptKnock can account for the thermodynamic viability of the knockouts and examine how variations in metabolite concentrations affect the coupling. We have shown that the coupling between growth and byproduct formation can change in response to variations in concentrations. Thus, a knockout strategy might be optimal for one intracellular condition but suboptimal for another. If metabolomics data are available, TOptKnock can search for optimal knockout interventions under the given condition. We also envision that the TOptKnock framework will help develop strategies for manipulating metabolite concentrations to couple growth and byproduct formation.
A pipeline for facile cloning of antibody Fv domains and their expression, purification, and characterization as recombinant His-tagged IgGs
Authors: Sinha Akesh , Park Jinha M. , Gulzar Naveed , Pandya Darpan N. , Wadas Thaddeus J. , Scott Jamie K.
Published: February 2024

We report a functional pipeline for facile conversion of variable Fv domains, typically discovered in antibody discovery programs, into chimeric monoclonal antibodies (mAbs). Often, in initial screenings, a set of candidate mAbs is produced in small volumes and purified from supernatant for testing. Our pipeline also simplifies purification of mAbs by using an extended histidine tag (His-10) fused to the C-terminus of the light chain. Both the length of the His-10 and its location have been shown to affect the efficacy of mAb purification using an inexpensive nickel-based resin at neutral pH. Our antibody cloning and purification pipeline, when followed together with detection and affinity measurements, can be smoothly incorporated into an antibody discovery workflow.
Host-pathogen Coadaptation by running with PAR protein
Authors: Zhu Sucheng , Zhou Xinyi , Qi Bin
Published: February 2024

Host-pathogen coadaptation is mutually beneficial for the survival of both organisms. Embryo development is a crucial aspect of animal evolution as it ensures the continuation of their offspring. However, there is little understanding of the coadaptation mechanisms underlying embryo developmental factors in host-pathogen interactions. Here, by using aC. elegans-P. aeruginosainfection model, we demonstrate that PAR-5, essential for the establishment of anterior-posterior polarity within the single cellC. eleganszygote, acts as a mediator in regulating host-pathogen co-evolution. We discover thatPseudomonas aeruginosa-PA14 infection induces PAR-5 expression, which accelerates animal embryo development and ensures the continuity of their offspring. Moreover, PA14 stimulates host PAR-5 secretion, which reduces the virulence of PA14. Both functions of PAR-5 are beneficial for host survival. Meanwhile, pathogens utilize PAR-5 to inhibit host immunity/UPRERby bypassing the core PMK-1-mediated innate immunity and activating mTOR by interacting with LET-363, promoting pathogen spread. Therefore, our study uncovers an unexpected mechanism in host-pathogen co-evolution that targets a host embryo developmental factor, promoting coexistence and facilitating the adaptation of both hosts and pathogens.
DNA metabarcoding diet analysis in ruminants is quantitative and integrates feeding over several weeks
Authors: Kamenova Stefaniya , Meyer Pernille , Brysting Anne Krag , Rescia Leo , Folkow Lars P. , Sundset Monica Alterskjær , Coissac Éric , Gussarova Galina
Published: February 2024

Dietary DNA metabarcoding is an established method, especially useful for resolving the diverse diets of large mammalian herbivores (LMH). However, despite longstanding research interest on the topic, we still lack unequivocal evidence on the potential of DNA metabarcoding to reflect proportions of ingested dietary plants in LMH. One major aspect to consider is the time window during which ingested diet remains detectable in faecal samples. This parameter is currently unknown for LMH, thus potentially hindering the scope of ecological conclusions. Another unknown factor is quantitative performance, i.e. the extent to which the amount of ingested biomass can be assessed based on sequence read abundances. We assessed DNA metabarcoding quantitative performance and DNA half-life detectability for plants with different digestibilities in a controlled feeding experiment with three female Eurasian tundra reindeer (Rangifer tarandus tarandus). Reindeer were fed birch twigs (Betula pubescens) and increasing biomass of lichen (mainlyCladonia stellaris). Relative read abundance positively correlated with ingested lichen biomass, suggesting potential for deriving dietary proportions in free-ranging reindeer on natural pastures. Dietary DNA was consistently detected within a few hours upon ingestion, with a mean half-life detectability of 30 and 14 hours for birch and lichen, respectively. However, dietary DNA remained detectable in faeces for at least 26 days post-feeding, indicating that a single faecal sample can provide an unsuspectedly integrative estimate of diet in ruminants. Together, our findings provide novel empirical validation of DNA metabarcoding as a tool for diet analysis in LMH.
A multipleArc(mArc) tagging system to uncover the organizational principles of multiple memories
Authors: Stackmann Michelle , Yelhekar Tushar D. , Meng Meizhen , Sun Xiaochen , Nthumba Joseph , Bulthuis Nicholas E. , Vaughan Nick , Zhu Elaine , Lin Yingxi , Denny Christine A.
Published: February 2024

Engrams or memory traces are the neuronal ensembles that collectively store individual experiences. Genetic strategies based on immediate early genes (IEGs), such asArc/Arg3.1, allow us to tag the ensembles active during memory encoding and compare them to those active during retrieval. However, these strategies only allow for the tagging of one neural ensemble. Here, we developed a multipleArc(mArc) system that allows for the tagging of twoArc+ensembles. We validated this system by investigating how context, time, and valence influence neuronal ensemble reactivation in the dentate gyrus (DG). We show that similar contextual and valenced experiences are encoded in overlapping DG ensembles. We also find that ensembles are modulated by time, where experiences closer in time are encoded in more similar ensembles. These results highlight the dynamic nature of DG ensembles and show that the mArc system provides a powerful approach for investigating multiple memories in the brain.

HIGHLIGHTS

The mArc system allows for the tagging of twoArc+ensembles in the same mouse

DG ensembles labeled by the mArc system receive increased excitatory input

Context, valence, and time influence DG ensemble reactivation

DG neural ensembles are reactivated less with increasing time
Quality of life in head and neck cancer survivors: the Big Data for Quality of Life study
Authors: Moreira-Soares Mauricio , Fossen Erlend I. F. , Taylor Katherine J. , Singer Susanne , Hurley Katrina , Thomas Steve , Pring Miranda , Ness Andrew , Cavalieri Stefano , Vener Claudia , Lopez-Perez Laura , Cabrera-Umpierrez Maria Fernanda , Fico Giuseppe , Frigessi Arnoldo , Licitra Lisa , LeBlanc Marissa
Published: February 2024

Background

The Big Data for Quality of Life (BD4QoL) study investigates quality of life (QoL) in head and neck cancer (HNC) survivors, focusing on survivorship and characterizing survivor demographics.

Methods

We screened data from 5 studies across Europe (N=7276) and included patients with a diagnosis of squamous cell carcinoma (oral cavity, hypopharynx, larynx, oropharynx, nasal cavity and paranasal sinuses), treated with curative intent, alive after treatment, TNM 7thed. stages I, II, III, IVa and IVb, with availability of QoL questionnaires.

Results

The cohort of 4448 HNC survivors primarily includes men (78%) with median age 61 years. Most received radiotherapy (75%) and had a history of smoking (78%). Survivors’ scores on EORTC QLQ-C30 functioning scales indicated high functioning, with prevalent symptoms of fatigue, pain, and insomnia. Lower rates of missing data were observed in older patients, those with higher education and income levels, nonsmokers, married individuals, and patients not treated with radiotherapy. The odds ratios ranged from 0.47 to 0.99, indicating these factors may predict more consistent QoL data reporting in HNC survivors.

Conclusions

These data support the development and validation of clinical prediction models for QoL in HNC survivors in a multicentre randomized controlled trial.
WITHDRAWN: Comparison of Leucocyte Telomere Length, Atherosclerotic Cardiovascular disease risk and the output of a Deep learning Cardiac BioAge risk prediction tool: A UK Biobank Cohort study
Authors: Vaghefi Ehsan , An Songyang , Corbett Rini , Squirrell David
Published: February 2024

Withdrawal Statement

“The authors have withdrawn their manuscript owing to major updates that will be made prior to resubmission. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.”
Recapitulating memory B cell responses in a Lymphoid Organ-Chip to evaluate mRNA vaccine boosting strategies
Authors: Jeger-Madiot Raphaël , Planas Delphine , Staropoli Isabelle , Kervevan Jérôme , Mary Héloïse , Collina Camilla , Fonseca Barbara F. , Debarnot Hippolyte , Robinot Rémy , Gellenoncourt Stacy , Schwartz Olivier , Ewart Lorna , Bscheider Michael , Gobaa Samy , Chakrabarti Lisa A.
Published: February 2024

Predicting the immunogenicity of candidate vaccines in humans remains a challenge. To address this issue, we developed a Lymphoid Organ-Chip (LO chip) model based on a microfluidic chip seeded with human PBMC at high density within a 3D collagen matrix. Perfusion of the SARS-CoV-2 Spike protein mimicked a vaccine boost by inducing a massive amplification of Spike-specific memory B cells, plasmablast differentiation, and Spike-specific antibody secretion. Features of lymphoid tissue, including the formation of activated CD4+ T cell/B cell clusters and the emigration of matured plasmablasts, were recapitulated in the LO chip. Importantly, myeloid cells were competent at capturing and expressing mRNA vectored by lipid nanoparticles, enabling the assessment of responses to mRNA vaccines. Comparison of on-chip responses to Wuhan monovalent and Wuhan/Omicron bivalent mRNA vaccine boosts showed equivalent induction of Omicron neutralizing antibodies, pointing at immune imprinting as reportedin vivo. The LO chip thus represents a versatile platform suited to the preclinical evaluation of vaccine boosting strategies.
Independent regulation of early trafficking of NMDA receptors by ligand-binding domains of the GluN1 and GluN2A subunits
Authors: Netolicky Jakub , Zahumenska Petra , Misiachna Anna , Kolcheva Marharyta , Kucera Tomas , Fibigar Jakub , Rehakova Kristyna , Hemelikova Katarina , Kortus Stepan , Langore Emily , Ladislav Marek , Korabecny Jan , Horak Martin
Published: February 2024

The essential role of N-methyl-D-aspartate receptors (NMDARs) in excitatory neurotransmission is underscored by numerous pathogenic variants in the GluN subunits, including those identified in their ligand-binding domains (LBDs). The prevailing hypothesis postulates that the endoplasmic reticulum (ER) quality control machinery verifies the agonist occupancy of NMDARs; however, whether it controls the structure of LBDs or the functionality of NMDARs is unknown. Using alanine substitutions combined with microscopy and electrophysiology, we found that surface expression of GluN1/GluN2A receptors, the primary NMDAR subtype in the adult forebrain, strongly correlates with EC50values for glycine and L-glutamate. Interestingly, co-expression of both GluN1 and GluN2A subunits with alanine substitutions led to an additive reduction in the surface number of GluN1/GluN2A receptors, as did co-expression of both GluN1 and GluN2A subunits containing closed cleft conformation of LBDs. The synchronized ER release confirmed the altered regulation of early trafficking of GluN1/GluN2A receptors bearing alanine substitutions in the LBDs. Furthermore, the human versions of GluN1/GluN2A receptors containing pathogenic GluN1-S688Y, GluN1-S688P, GluN1-D732E, GluN2A-S511L, and GluN2A-T690M variants exhibited distinct surface expression compared to the corresponding alanine substitutions. Mutant cycles of GluN1-S688, GluN1-D732, GluN2A-S511, and GluN2A-T690 residues revealed, in most cases, a weak correlation between surface expression of the mutant GluN1/GluN2A receptors and their EC50values for glycine or L-glutamate. Consistent with our experimental data, molecular modeling and dynamics showed that the ER quality control machinery likely perceives structural changes of the LBDs but not the functionality of GluN1/GluN2A receptors.

Significant statement

Our study showed that structural changes in LBDs independently regulate the early trafficking of GluN1/GluN2A receptors and that the surface numbers of mutant GluN1/GluN2A receptors do not necessarily correlate with their agonist sensitivity. In addition, we validated a novel system of synchronized release of GluN1/GluN2A receptors from the ER. Together, our experimental andin silicofindings support the urgency of further detailed research on the regulation of early trafficking of NMDARs, as it may open the avenue to targeted therapeutic intervention of CNS disorders associated with pathogenic variants in GluN subunits.
Taurine pangenome uncovers a segmental duplication upstream ofKITassociated with depigmentation in white-headed cattle
Authors: Milia Sotiria , Leonard Alexander S. , Mapel Xena Marie , Ulloa Sandra Milena Bernal , Drögemüller Cord , Pausch Hubert
Published: February 2024

Cattle have been selectively bred for coat color, spotting, and depigmentation patterns. The assumed autosomal dominant inherited genetic variants underlying the characteristic white head of Fleckvieh, Simmental, and Hereford cattle have not been identified yet, although the contribution of structural variation upstream theKITgene has been proposed. Here, we construct a graph pangenome from 24 haplotype assemblies representing seven taurine cattle breeds to identify and characterize the white head-associated locus for the first time based on long-read sequencing data and pangenome analyses. We introduce a pangenome-wide association mapping approach which examines assembly path similarities within the graph to reveal an association between two most likely serial alleles of a complex structural variant 66 kb upstreamKITand facial depigmentation. The complex structural variant contains a variable number of tandemly duplicated 14.3 kb repeats, consisting of LTRs, LINEs, and other repetitive elements, leading to misleading alignments of short and long reads when using a linear reference. We align 250 short-read sequencing samples spanning 15 cattle breeds to the pangenome graph, further validating that the alleles of the structural variant segregate with head depigmentation. We estimate an increased count of repeats in Hereford relative to Simmental and other white-headed cattle breeds from the graph alignment coverage, suggesting a large under-assembly in the current Hereford-based cattle reference genome which had fewer copies. We show that exploiting assembly path similarities within graph pangenomes can reveal trait-associated complex structural variants.
Wheat NAC transcription factorNAC5-1is a positive regulator of senescence
Authors: Evans Catherine , Mogg Sophie Louise , Soraru Charline , Wallington Emma , Coates Juliet , Borrill Philippa
Published: February 2024

Wheat (Triticum aestivumL.) is an important source of both calories and protein in global diets, but there is a trade-off between grain yield and protein content. The timing of leaf senescence could mediate this trade-off as it is associated with both decline in photosynthesis and nitrogen remobilisation from leaves to grain. NAC transcription factors play key roles in regulating senescence timing. In rice,OsNAC5expression is correlated with earlier senescence, but the role of the wheat ortholog in senescence had not been characterised. We verified thatNAC5-1is the ortholog ofOsNAC5and that it is expressed in senescing flag leaves in wheat. To characteriseNAC5-1,we combined missense mutations inNAC5-A1andNAC5-B1from a TILLING mutant population and overexpressedNAC5-A1in wheat. Mutation inNAC5-1was associated with delayed onset of flag leaf senescence, while overexpression ofNAC5-A1was associated with slightly earlier onset of leaf senescence. DAP-seq was performed to locate transcription factor binding sites ofNAC5-1.Analysis of DAP-seq and comparison with other studies identified putative downstream target genes ofNAC5-1which could be associated with senescence. This work showed thatNAC5-1is a positive transcriptional regulator of leaf senescence in wheat. Further research is needed to test the effect ofNAC5-1on yield and protein content in field trials, to assess the potential to exploit this senescence regulator to develop high-yielding wheat while maintaining grain protein content.
Serotonin drives aggression and social behaviours of laboratory mice in a semi-natural environment
Authors: Rivalan Marion , Alonso Lucille , Mosienko Valentina , Bey Patrik , Hyde Alexia , Bader Michael , Winter York , Alenina Natalia
Published: February 2024

Aggression is an adaptive social behaviour crucial for the stability and prosperity of social groups. When uncontrolled, aggression leads to pathological violence that disrupts group structure and individual well-being. The comorbidity of uncontrolled aggression across different psychopathologies makes it a potential endophenotype of mental disorders with the same neurobiological substrates. Serotonin plays a critical role in the regulation of impulsive and aggressive behaviours, and mice lacking brain serotonin, due to the ablation of a rate-limiting enzyme of serotonin synthesis (Tryptophan hydroxylase 2, TPH2), are a potential model of pathological aggression. Home cage monitoring allows for the continuous observation and quantification of social and non-social behaviours in group-housed, freely-moving mice. Using an ethological approach, we investigated the impact of central serotonin ablation on everyday expression of social and non-social behaviours and their correlations in undisturbed, group-livingTph2-deficient and wildtype mice. By training a machine learning algorithm on behavioural time series, “allogrooming”, “struggling at feeder” and “eating” emerged as key behaviours dissociating one genotype from the other. AlthoughTph2-deficient mice showed characteristics of pathological aggression and decreased communication compared to wildtype animals they still showed affiliative behaviours to normal levels. Altogether, such distinct and dynamic phenotype of Tph2-deficient mice influenced the group’s structure and the dynamic of its hierarchical organization which emerged later. These aspects were analyzed using social network analysis and the Glicko rating methods. This study demonstrates the importance of the ethological approach for understanding the global impact of pathological aggression on different aspects of life both at the individual and the group level. Home cage monitoring allows the observation of the natural behaviours of the mice in a semi-natural habitat and provides an accurate representation of real-world phenomena and pathological mechanisms. The results of this study provide insights into the neurobiological substrate of pathological aggression and their potential role in complex brain disorders.
A spatial model of autophosphorylation of Ca2+/calmodulin-dependent protein kinase II (CaMKII) predicts that the lifetime of phospho-CaMKII after induction of synaptic plasticity is greatly prolonged by CaM-trapping
Authors: Bartol Thomas M. , Ordyan Mariam , Sejnowski Terrence J. , Rangamani Padmini , Kennedy Mary B.
Published: February 2024

Long-term potentiation (LTP) is a biochemical process that underlies learning in excitatory glutamatergic synapses in the Central Nervous System (CNS). The critical early driver of LTP is autophosphorylation of the abundant postsynaptic enzyme, Ca2+/calmodulin-dependent protein kinase II (CaMKII). Autophosphorylation is initiated by Ca2+flowing through NMDA receptors activated by strong synaptic activity. Its lifetime is ultimately determined by the balance of the rates of autophosphorylation and of dephosphorylation by protein phosphatase 1 (PP1). Here we have modeled the autophosphorylation and dephosphorylation of CaMKII during synaptic activity in a spine synapse using MCell4, an open source computer program for creating particle-based stochastic, and spatially realistic models of cellular microchemistry. The model integrates four earlier detailed models of separate aspects of regulation of spine Ca2+and CaMKII activity, each of which incorporate experimentally measured biochemical parameters and have been validated against experimental data. We validate the composite model by showing that it accurately predicts previous experimental measurements of effects of NMDA receptor activation, including high sensitivity of induction of LTP to phosphatase activityin vivo,and persistence of autophosphorylation for a period of minutes after the end of synaptic stimulation. We then use the model to probe aspects of the mechanism of regulation of autophosphorylation of CaMKII that are difficult to measurein vivo. We examine the effects of “CaM-trapping,” a process in which the affinity for Ca2+/CaM increases several hundred-fold after autophosphorylation. We find that CaM-trapping does not increase the proportion of autophosphorylated subunits in holoenzymes after a complex stimulus, as previously hypothesized. Instead, CaM-trapping may dramatically prolong the lifetime of autophosphorylated CaMKII through steric hindrance of dephosphorylation by protein phosphatase 1. The results provide motivation for experimental measurement of the extent of suppression of dephosphorylation of CaMKII by bound Ca2+/CaM. The composite MCell4 model of biochemical effects of complex stimuli in synaptic spines is a powerful new tool for realistic, detailed dissection of mechanisms of synaptic plasticity.