bluuebunny/crossref_metadata_2025 huggingface dataset:
PRC1 and CTCF-Mediated Transition from Poised to Active Chromatin Loops Drives Bivalent Gene Activation
Authors: Hanafiah Aflah , Geng Zhuangzhuang , Liu Tingting , Tai Yen Teng , Cai Wenjie , Wang Qiang , Christensen Neil , Liu Yan , Yue Feng , Gao Zhonghua
Published: November 2024

Polycomb Repressive Complex 1 (PRC1) and CCCTC-binding factor (CTCF) are critical regulators of 3D chromatin architecture that influence cellular transcriptional programs. Spatial chromatin structures comprise conserved compartments, topologically associating domains (TADs), and dynamic, cell-type-specific chromatin loops. Although the role of CTCF in chromatin organization is well-known, the involvement of PRC1 is less understood. In this study, we identified an unexpected, essential role for the canonical Pcgf2-containing PRC1 complex (cPRC1.2), a known transcriptional repressor, in activating bivalent genes during differentiation. Our Hi-C analysis revealed that cPRC1.2 forms chromatin loops at bivalent promoters, rendering them silent yet poised for activation. Using mouse embryonic stem cells (ESCs) with CRISPR/Cas9-mediated gene editing, we found that the loss of Pcgf2, though not affecting the global level of H2AK119ub1, disrupts these cPRC1.2 loops in ESCs and impairs the transcriptional induction of crucial target genes necessary for neuronal differentiation. Furthermore, we identified CTCF enrichment at cPRC1.2 loop anchors and at Polycomb group (PcG) bodies, nuclear foci with concentrated PRC1 and its tethered chromatin domains, suggesting that PRC1 and CTCF cooperatively shape chromatin loop structures. Through virtual 4C and other genomic analyses, we discovered that establishing neuronal progenitor cell (NPC) identity involves a switch from cPRC1.2-mediated chromatin loops to CTCF-mediated active loops, enabling the expression of critical lineage-specific factors. This study uncovers a novel mechanism by which pre-formed PRC1 and CTCF loops at lineage-specific genes maintain a poised state for subsequent gene activation, advancing our understanding of the role of chromatin architecture in controlling cell fate transitions.
Language model-guided anticipation and discovery of unknown metabolites
Authors: Qiang Hantao , Wang Fei , Lu Wenyun , Xing Xi , Kim Hahn , Merette Sandrine A.M. , Ayres Lucas B. , Oler Eponine , AbuSalim Jenna E. , Roichman Asael , Neinast Michael , Cordova Ricardo A. , Lee Won Dong , Herbst Ehud , Gupta Vishu , Neff Samuel , Hiebert-Giesbrecht Mickel , Young Adamo , Gautam Vasuk , Tian Siyang , Wang Bo , Röst Hannes , Greiner Russell , Chen Li , Johnston Chad W. , Foster Leonard J. , Shapiro Aaron M. , Wishart David S. , Rabinowitz Joshua D. , Skinnider Michael A.
Published: November 2024

Despite decades of study, large parts of the mammalian metabolome remain unexplored. Mass spectrometry-based metabolomics routinely detects thousands of small molecule-associated peaks within human tissues and biofluids, but typically only a small fraction of these can be identified, and structure elucidation of novel metabolites remains a low-throughput endeavor. Biochemical large language models have transformed the interpretation of DNA, RNA, and protein sequences, but have not yet had a comparable impact on understanding small molecule metabolism. Here, we present an approach that leverages chemical language models to discover previously uncharacterized metabolites. We introduce DeepMet, a chemical language model that learns the latent biosynthetic logic embedded within the structures of known metabolites and exploits this understanding to anticipate the existence of as-of-yet undiscovered metabolites. Prospective chemical synthesis of metabolites predicted to exist by DeepMet directs their targeted discovery. Integrating DeepMet with tandem mass spectrometry (MS/MS) data enables automated metabolite discovery within complex tissues. We harness DeepMet to discover several dozen structurally diverse mammalian metabolites. Our work demonstrates the potential for language models to accelerate the mapping of the metabolome.
Redefining the spliceosomal introns of the sexually transmitted parasiteTrichomonas vaginalisand its close relatives in columbid birds
Authors: Callejas-Hernández Francisco , Shiratori Mari , Sullivan Steven A. , Blow Frances , Carlton Jane M.
Published: November 2024

Trichomonas vaginalisinfects the urogenital tract of men and women and causes the sexually transmitted infection trichomoniasis. Since the publication of its draft genome in 2007, the genome has drawn attention for several reasons, including its unusually large size, massive expansion of gene families, and high repeat content. The fragmented nature of the draft assembly made it challenging to obtain accurate metrics of features, such as spliceosomal introns. The number of introns identified varied over the years, ranging from 41 when first characterized in 2005, to 32 in 2018 when the repertoire was revised. In both cases, the results suggested that more introns could be present in the genome. In this study, we exploited our newT. vaginalisG3 chromosome-scale assembly and annotation and high-coverage transcriptome datasets to provide a definitive analysis of the complete repertoire of spliceosomal introns in the species. We developed a custom pipeline that distinguishes true splicing events from chimeric alignments by utilizing the extended motifs required by the splicing machinery and experimentally verified the results using transcript evidence. We identified a total of 63 active introns and 34 putative “inactive” intron sequences inT. vaginalis, enabling an analysis of their length distribution, extended consensus motifs, intron phase distribution (including an unexpected expansion of UTR introns), and functional annotation. Notably, we found that the shortest intron inT. vaginalis, at only 23 nucleotides in size, is one of the shortest introns known to date. We tested our pipeline on a chromosome-scale assembly of the bird parasiteTrichomonas stableri, the closest known relative toT. vaginalis. Our results revealed some conservation of the main features (total intron count, sequence, length distribution, and motifs) of these two closely related species, although differences in their functional annotation and duplication suggest more specialized splicing machinery inT. vaginalis.
Uncertainty-aware genomic deep learning with knowledge distillation
Authors: Zhou Jessica , Rizzo Kaeli , Tang Ziqi , Koo Peter K
Published: November 2024

Deep neural networks (DNNs) have advanced predictive modeling for regulatory genomics, but challenges remain in ensuring the reliability of their predictions and understanding the key factors behind their decision making. Here we introduce DEGU (Distilling Ensembles for Genomic Uncertainty-aware models), a method that integrates ensemble learning and knowledge distillation to improve the robustness and explainability of DNN predictions. DEGU distills the predictions of an ensemble of DNNs into a single model, capturing both the average of the ensemble’s predictions and the variability across them, with the latter representing epistemic (or model-based) uncertainty. DEGU also includes an optional auxiliary task to estimate aleatoric, or data-based, uncertainty by modeling variability across experimental replicates. By applying DEGU across various functional genomic prediction tasks, we demonstrate that DEGU-trained models inherit the performance benefits of ensembles in a single model, with improved generalization to out-of-distribution sequences and more consistent explanations of cis-regulatory mechanisms through attribution analysis. Moreover, DEGU-trained models provide calibrated uncertainty estimates, with conformal prediction offering coverage guarantees under minimal assumptions. Overall, DEGU paves the way for robust and trustworthy applications of deep learning in genomics research.
Rate ofde novomutations in the three-spined stickleback
Authors: Zhang Chaowei , Reid Kerry , Schierup Mikkel Heide , Wang Hongbo , Candolin Ulrika , Merilä Juha
Published: November 2024

Being a fundamentally important genetic parameter and evolutionary force, estimates of germline mutation rates have many uses in evolutionary biology. However, accurate estimates ofde novomutation (DNM) rates are still relatively scarce even for extensively studied evolutionary biology models. We estimated DNM rates for the three-spined stickleback (Gasterosteus aculeatus), the ‘supermodel’ of ecology and evolutionary biology. Using a large number of family trios sequenced to depth of 45x coverage, we identified 115 unique mutations genome wide and estimated the DNM rate atµ= 5.05 × 10-9/bp/gen without any detectable sex bias. The localised DNM rate was found to be positively correlated with recombination rate supporting the notion that recombination is a mutagenic process. Comparison ofµand genomic characteristics to those of the related nine-spined stickleback (Pungitius pungitius) revealed a high degree of similarity suggesting that despite 17.5 million years of independent evolution, the mutational processes in the two species appear to have been conserved.
Validation of an innovative two-part algorithm for detecting self-propulsion in manual wheelchair users
Authors: Gagnon Rose , Best Krista L. , Routhier François
Published: November 2024

Introduction

Actimetry is increasingly used to measure physical activity (PA) for MWC users. However, conversion of raw data into interpretable PA outcomes remains imprecise, and the differentiation between propulsion and non-propulsion is challenging. Using a previously developed two-part algorithm, the objectives of this study were to 1) measure the accuracy of total distance collected, and 2) validate the algorithm’s accuracy in differentiating between self-propulsion and non-propulsion.

Methods

Experimental study consisting of two data collection sessions. Actimetry data (Actigraph) were collected indoors (controlled conditions) during 100 repetitions (n=40 MWC propulsion, n=60 pushing the MWC) over three distances (10, 50 and 100 meters). Actimetry data (Actigraph) were also collected outdoors (uncontrolled condition) during self-propulsion over 1,000 meters (10 repetitions). Descriptive statistics (e.g., mean, standard deviation) with confidence intervals and accuracy measures (percentage of true value) were conducted for each trial.

Results

The algorithm measured total distance covered indoors with an excellent accuracy (98.9% to 99.8%). It differentiated between self-propulsion and non-propulsion with an accuracy between 96.2% and 99.2% under controlled condition, and between 91.3% and 100.0% under uncontrolled condition.

Conclusions

The algorithm tested allowed precise measurement of total distance covered, as well as an excellent discrimination between self-propulsion and non-propulsion.
A Mass Casualty Event in a Gaza War Hospital
Authors: Alsalqawi Abdalkarim , Abu Tahoon Khader , Nijim Adnan , Halimy Mohammed , Villar Richard
Published: November 2024

This study examines the impact of a mass casualty event (MCE) on a Gaza hospital during a military operation in June 2024, highlighting unique challenges encountered in conflict-zone medical care. The research analyses 47 casualties received by the Shuhada al-Aqsa Hospital in Deir-al-Balah, Gaza, over a concentrated period. Data collected include demographics, injury types, and pre-hospital and emergency department treatment delays. Findings reveal a predominance of blast injuries (76.6%), with compound injuries being present in 78.7% of casualties, resulting in a high injury burden (mean 1.68 injuries per casualty). The mean age of all casualties was 30.57 years. Mortality reached 14.89%, with females disproportionately affected, comprising 71.43% of fatalities. Transportation delays averaged 18.7 minutes, often without pre-arrival notification, underscoring logistical challenges in the Gaza conflict setting. In-hospital delays for treatment averaged 17.4 minutes. Gender disparities in trauma outcomes suggest biological and sociocultural factors influencing survival rates. The study emphasises the need for conflict-sensitive, gender-informed medical interventions, improved trauma care resources, and pre-hospital coordination protocols. This work aims to inform international medical volunteers on the realities of conflict-zone healthcare and support system-level improvements in MCE responses in resource-limited settings.
Comprehensive analysis of key m6A RNA modification-related genes and immune infiltrates in hypertrophic cardiomyopathy
Authors: Hu Xia , Liang Bo
Published: November 2024

Hypertrophic cardiomyopathy (HCM) is the most common inherited heart disease. We performed a comprehensive analysis to construct the correlation of m6A and immune in HCM. Two HCM datasets (GSE141910 and GSE160997) and m6A-related regulators were obtained from GEO and published articles, respectively. Differentially expressed m6A-related regulators were obtained. Random forest model and nomogram were conducted to assess the risk of HCM, and finally, the m6A subtype was constructed. Functional enrichment analysis was conducted. Protein-protein interaction network of differentially expressed genes between m6A subtypes was performed. Furthermore, we constructed the Hubgene-chemical network, Hubgene-microRNA network, and Hubgene-transcription factor network of the top 10 hubgenes. Additionally, the immune subtype and hubgene subtype were constructed. PCR was performed to validate the m6A-related regulators. We obtained 20 m6A-related regulators in HCM. Among them, 8 m6A-related regulators differentially expressed (YTHDC1, HNRNPC, and FMR1 were up-regulated while YTHDC2, FTO, WTAP, IGF2BP2, and IGF2BP3 were down-regulated). FTO, FMR1, IGF2BP3, YTHDC1, and IGF2BP2 were the top 5 important m6A-related regulators and were used to conduct the nomogram. We obtained 329 differentially expressed genes in m6A subtype and these genes enriched HCM-related processes and pathways. Furthermore, we constructed the Hubgene-chemical network, Hubgene-microRNA network, and Hubgene-transcription factor network of the top 10 hubgenes (NFKBIA, NFKB1, PSMA3, PSMC4, PSMA2, PSMA4, PSMD7, PSMD10, PSMD8, and PSMA6). And then we constructed an immune subtype based on the immune cell infiltration levels and hubgene subtype based on the expression of the top 10 hubgenes. Finally, we verified the main results through experiments. In conclusion, we built a nomogram and identified 8 m6A-related regulators and 10 hubgenes, which were prominently associated with HCM. We found that m6A and the immune system may play a crucial role in the HCM. Accordingly, those genes and pathways might become therapeutic targets with clinical usefulness in the future.
Gompertz law based biological age (GOLD BioAge): a simple and practical measurement of biological aging to capture morbidity and mortality risks
Authors: Hao Meng , Zhang Hui , Wu Jingyi , Li Xiangnan , Huang Yaqi , Wang Meijia , Wang Shuming , Wang Jiaofeng , Chen Jie , Bao Zhi jun , Jin Li , Wang Xiaofeng , Hu Zixin , Jiang Shuai , Li Yi
Published: November 2024

Biological age reflects actual aging and overall health, but current aging clocks are often complex and difficult to interpret, limiting their clinical application. In this study, we introduced a Gompertz law-based biological age (GOLD BioAge) model that simplified aging assessment. We estimated GOLD BioAge using clinical biomarkers and found significant associations of the difference from chronological age (BioAgeDiff) with risks of morbidity and mortality in NHANES. Moreover, we developed GOLD ProtAge and MetAge using proteomics and metabolomics data, which outperformed the clinical-only model in predicting mortality and chronic disease risks in UK Biobank. Benchmark analysis illustrated that our models exceeded common aging clocks in predicting mortality across diverse age groups in both NHANES and UK Biobank. The results demonstrated that the GOLD BioAge algorithm effectively applied to both clinical and omics data, showing excellent performance in predicting age-related outcomes. Additionally, we created a simplified version called the Light BioAge, which used three biomarkers for aging assessment. The Light model reliably captured mortality risks in three validation cohorts (CHARLS, RuLAS, CLHLS). It significantly predicted the onset of frailty, stratified frail individuals, and collectively identified individuals at high risk of mortality. In summary, the algorithm of GOLD BioAge could provide a valuable framework for aging assessment in public health and clinical practice.

Highlights

The algorithm of Gompertz law based biological age (GOLD BioAge) was proposed to construct biological aging clocks with convenient and interpretable calculations, which had better performance in predicting mortality risks.

Our approach was applicable to proteomics and metabolomics, yielding ProtAge and MetAge with great clinical prospect to improve accuracy of aging assessment and prevent age-related diseases.

The Light BioAge, a simplified version, was developed using age and three biomarkers, and it independently predicted mortality in three cohorts.

The Light BioAgeDiff significantly predicted the onset of frailty, stratified frail individuals, and collectively identified individuals at high risk of mortality.
Dexmedetomidine as an Adjunctive Sedative in Patients Undergoing Endoscopic Submucosal Dissection: A Systematic Review and Meta-Analysis
Authors: Abosheaishaa Hazem , Abdallfatah Abdallfatah , Abdelghany Abdelmalek , Sethi Arshia , Ismail Abdellatif , Mohamed Doha , Aboeldahb Moataz , Abdelhalim Omar , Mohamed Islam , Azzam Ahmed Y. , Essibayi Muhammed Amir , Altschul David J. , Nassar Mahmoud , Bilal Mohammad
Published: November 2024

Introduction

Endoscopic submucosal dissection (ESD) allows for curative en-bloc resection of dysplastic gastrointestinal (GI) tract lesions. However, it is associated with postoperative adverse events (AEs) such as pain, bleeding, and perforation. Dexmedetomidine, an α2-receptor agonist, has emerged as a promising adjunct sedative for ESD under moderate sedation, offering anxiolysis and analgesia. We conducted a systematic review and meta-analysis to evaluate its efficacy and safety for use in ESD.

Methods

A comprehensive systematic search was conducted across multiple databases, including Embase, Medline, Scopus, and Web of Science. Studies that involved ESD utilizing dexmedetomidine as an adjunctive medication in combination with other sedatives, were included. Data extraction and risk of bias assessment were independently performed by two reviewers. Meta-analysis was carried out with RevMan using a random-effects model.

Results

Eight studies were included in the final analysis. Dexmedetomidine showed no significant difference in en-bloc or complete resection rates compared to controls. Sedation and procedure times were similar between the two groups as well. Dexmedetomidine significantly reduced restlessness (OR 0.15, 95% CI:0.07 to 0.29) and increased bradycardia (OR 7.15, 95% CI 3.17 to 16.11) compared to controls. Upon subgroup analysis, Dexmedetomidine plus Propofol, and Dexmedetomidine plus Midazolam, revealed the same findings regarding restlessness and bradycardia compared to controls which confirmed the adjunctive effects of Dexmedetomidine.

Conclusions

Dexmedetomidine as an adjunctive sedative appears safe and effective in ESD, reducing restlessness without significant adverse events. The risk of bradycardia is increased, which may be reflective of reduced physiological stress. Future studies should explore optimal dosing and compare Dexmedetomidine with other sedatives in diverse populations.
Humanace2andtmprss2polymorphisms for predicting susceptibility to tuberculosis and COVID-19 co-infection in Cameroonian cohort
Authors: Kameni Mary Ngongang , Tchoupe Eric Berenger , Kamdem Severin Donald , Bhalla Nikhil , Jean Paul Assam Assam , Arnaud Tepa Njiguet , Neba Fuh Roger , Nanda Ranjan Kumar , Awuah Anthony Afum-Adjei , Amuasi John , Netongo Palmer Masumbe
Published: November 2024

SARS-CoV-2 andMycobacterium tuberculosis(Mtb) share similarities in their modes of transmission, pathophysiological symptoms, and manifestations. An imbalance in the immune response characterized by significantly elevated levels of some inflammatory cytokines may increase the risk of developing both tuberculosis (TB) and COVID-19 as a comorbid condition. The role of SNPs inace2andtmprss2conferring higher susceptibility to TB-COVID-19 co-infection is relatively underexplored. In this study, a Cameroonian cohort consisting of COVID-19-infected (n = 31), TB-infected (n = 43), TB-COVID-19 co-infected (n = 21), and a control group (n = 24) was studied. The immune response and disease severity were estimated by quantitating inflammatory cytokine levels and self-reported and clinically diagnosed symptoms. We identified SNPs inace2andtmprss2genes previously associated with COVID-19 susceptibility and assessed their association with comorbid conditions. We identified genotypes (Allele AG: rs147311723, rs35803318; Allele AA: rs2074192; Allele CG: rs4240157; Allele AG: rs4646179) inace2gene and (Allele CA: rs61735791, Allele CT: rs12329760) intmprss2genes that are putatively associated with higher susceptibility to both TB and COVID-19. This study underscores the significant genetic and immunological factors contributing to susceptibility to TB and COVID-19 co-infections.
Direct Oral Anticoagulants vs. Heparin for Cancer-Related Stroke: Augmented Meta-Analysis
Authors: Essibayi Muhammed Amir , Azzam Ahmed Y. , Sener Ugur , Altschul David , Atik Merve , Keser Zafer
Published: November 2024

Background

Ischemic stroke is common among patients with systemic malignancy, associated with increased risk of neurological deterioration and mortality compared to the general population. Optimal approach to secondary stroke prevention in cancer patients is unclear. In this meta-analysis, we evaluated available data on the use of direct oral anticoagulants (DOACs) and heparin products for stroke prevention in this population.

Methods

Using the Nested Knowledge AutoLit software, we performed PubMed search in September 2023 for articles reporting the use of antithrombotics for cancer-associated stroke. We conducted systematic review and meta-analysis. We also used a novel computational augmentation method to amplify the sample size to predict the effect before and after sample size augmentation and predict the results of further trials.

Results

Among 253 potential studies screened, 7 were eligible for inclusion. 439 patients were treated with DOACs and 3968 with heparin products. Among patients treated with heparin, intracerebral hemorrhage (8.8 % vs 1.6, p=.02), overall hemorrhagic complications (17.9% vs 3.5%, p<.001), and mortality [28.1% vs 23.5%, p<.001] were respectively significantly higher than those reported among patients who received DOAC for cancer-associated ischemic stroke. No significant difference was observed in the rates of recurrent deep venous thrombosis, clinically significant hemorrhage, and clinical outcomes between the treatment groups. Similar results were shown with augmented meta-analysis.

Conclusions

This meta-analysis shows DOACs may have efficacy and safety profile similar to heparin products for recurrent stroke prevention in patients with cancer. Given the small number of studies and limited data, findings should be interpreted with caution.
Neuropathic Gastroduodenal Disorders can be Diagnosed by Non-Invasive Body Surface Gastric Mapping: a Comparison with Antroduodenal Manometry
Authors: Sadaka Christian , Xu Binghong , Benitez Alain J , Orians Carolyn M. , Bowerman Corey , Dourlain Jordan , Skaggs Beth , Konka Kimberly G. , Roshkovan Lexi , Humphrey Gayl , Calder Stefan , Schamberg Gabriel , O’Grady Greg , Gharibans Armen A , Mousa Hayat
Published: November 2024

Background

Antroduodenal manometry (ADM) is the gold standard for diagnosing myopathy and neuropathy in patients with upper gastrointestinal (GI) disorders. However, ADM is invasive and costly. Body surface gastric mapping (BSGM) has emerged as a non-invasive test to assess gastric function. This study evaluates the correlation between BSGM and ADM in children.

Methods

Clinically indicated ADM was performed using high-resolution water-perfused motility catheters, with simultaneous BSGM. Real-time symptoms were tracked using a validated symptom logging app at 15-min intervals, and Nausea Severity Scale (NSS) scores recorded. Protocols involved a 2 hour fast, provocative testing, a meal, and over 1 hr of postprandial recordings. ADM tracings were categorized into neuropathy, myopathy, postprandial hypomotility, or normal. BSGM metrics included principal gastric frequency, BMI-adjusted amplitude, and Rhythm Index. Gastric emptying data were also evaluated.

Results

Fifteen subjects were recruited (13 female; ages 10-19 years, BMI 20.6±3.5 kg/m2). ADM results showed neuropathy (n=4), myopathy (n=1), post-prandial hypomotility (n=4), and normal motility (n=6). Patients with neuropathy had lower rhythm stability (0.16±0.03 vs 0.38±0.17; p=.001), accompanied by higher nausea scores (8.2±1.2 vs 3.15±2.9; p<.001) and bloating (7.3±0.9 vs 2.1±2.0; p<.001). ADM neuropathy correlated completely with dysrhythmia on BSGM. Normal ADM were consistent with normal BSGM in 83.3% of cases. Delayed gastric emptying did not correlate with a neuropathic diagnosis.

Conclusion

Dysrhythmic BSGM phenotype reliably identified gastrointestinal neuropathy with identical results to ADM, with significant correlations to nausea and bloating severity. This study supports considering BSGM as an actionable biomarker when performing ADM is not feasible.

Key points

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Body Surface Gastric Mapping (BSGM) low stability phenotype correlated perfectly with neuropathy detected on Antroduodenal Manometry (ADM). The BSGM normal phenotype also showed a good correlation with normal ADM studies.

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BSGM low stability phenotype was linked to higher severity scores for nausea and bloating.

Abbreviations used: Antroduodenal Manometry (ADM), Body Surface Gastric Mapping (BSGM), Gastric Emptying Scintigraphy (GES), Gastroparesis (GP), Functional Dyspepsia (FD), Electrogastrography (EGG)
ALPK3 heterozygous truncating variants cause late-onset hypertrophic cardiomyopathy with frequent apical involvement and apical aneurysm
Authors: Busse Leora , Huth Emily A , Abraham Maria Roselle , Abraham Theodore , Padmanabhan Arun , Wojciak Julianne , Wright Gabrielle , Aatre Rajani , Campagna Rachel , Jackson Erika , Kreykes Sarah , Lane Kimberly , Sawyer Lindsey , Stevens Chelsea , Thomas Matthew , VanDyke Rebecca , Vedantham Vasanth , Higgs Emily J
Published: November 2024

Hypertrophic cardiomyopathy (HCM) is a genetically heterogeneous disorder with several established genotype-phenotype relationships. While biallelic truncating variants in theALPK3gene cause severe congenital HCM, recent studies have associated heterozygous truncating variants (ALPK3tv) with milder adult-onset HCM. Here we describe a multicenter cohort of 21 individuals with heterozygous ALPK3tv from 10 institutions in the United States, highlighting distinctive clinical characteristics compared to a control group of 132 patients with HCM caused by deleterious variants in sarcomeric genes. As compared to other HCM genotypes, ALPK3tv patients present at an older age (mean 57.25 years) with significantly lower left ventricular wall thickness (14.09 vs 19.78 mm with echocardiogram and 16.13 vs 21.13 mm with cardiac MRI), a lower prevalence of obstructive HCM (15% of ALPK3tv vs 45% of controls), and a strikingly higher incidence of apical aneurysm (22.22% vs. 2.40% in the control group). These results suggest a milder degree of hypertrophy in heterozygous ALPK3-related HCM as compared to other Mendelian causes of HCM, although the increased occurrence of apical aneurysms could have implications for ventricular arrhythmia risk. Our study underscores the importance of recognizing heterozygous ALPK3tv as a cause of adult-onset HCM and provides a comprehensive characterization of its clinical phenotype.
Dietary Restriction Enhances CD8⁺ T Cell Ketolysis to Limit Exhaustion and Boost Anti-Tumor Immunity
Authors: Oswald Brandon M. , DeCamp Lisa M. , Longo Joseph , Dahabieh Michael S. , Bunda Nicholas , Ma Shixin , Watson McLane J , Sheldon Ryan D. , Vincent Michael P. , Johnson Benjamin K. , Ellis Abigail E , Soper-Hopper Molly T. , Isaguirre Christine N , Shen Hui , Williams Kelsey S. , Crawford Peter A. , Kaech Susan , Jang H. Josh , Krawczyk Connie M. , Jones Russell G.
Published: November 2024

Reducing calorie intake without malnutrition limits tumor progression but the underlying mechanisms are poorly understood. Here we show that dietary restriction (DR) suppresses tumor growth by enhancing CD8+T cell-mediated anti-tumor immunity. DR reshapes CD8+T cell differentiation within the tumor microenvironment (TME), promoting the development of effector T cell subsets while limiting the accumulation of exhausted T (Tex) cells, and synergizes with anti-PD1 immunotherapy to restrict tumor growth. Mechanistically, DR enhances CD8+T cell metabolic fitness through increased ketone body oxidation (ketolysis), which boosts mitochondrial membrane potential and fuels tricarboxylic acid (TCA) cycle-dependent pathways essential for T cell function. T cells deficient for ketolysis exhibit reduced mitochondrial function, increased exhaustion, and fail to control tumor growth under DR conditions. Our findings reveal a critical role for the immune system in mediating the anti-tumor effects of DR, highlighting nutritional modulation of CD8+T cell fate in the TME as a critical determinant of anti-tumor immunity.
Developmental Stage and Cellular Context Determine Oncogenic and Molecular Outcomes ofEzh2Y641FMutation in Hematopoiesis
Authors: Zimmerman Sarah M. , Procasky Samantha J. , Smith Sofia R. , Liu Jie-Yu , Torrice Chad , Souroullas George P.
Published: November 2024

Mutations in the histone methyltransferase EZH2, particularly the Y641 hotspot mutation, have been implicated in hematologic malignancies, yet the effect of timing and cellular context on their oncogenic potential has remained unknown. In this study, we utilized a conditional allele with tissue-specific Cre drivers to investigate the effects ofEzh2Y641Fmutations at various stages of development, with a focus on the hematopoietic system. We found that ubiquitous heterozygousEzh2Y641Fexpression at birth, or conditional expression in hematopoietic or mesenchymal stem cells, led to decreased survival due to hematopoietic defects and bone marrow failure, with no evidence of malignancy. In contrast,Ezh2Y641Fexpression in committed B cells drives lymphoma formation, highlighting the lineage-specific oncogenic activity of the mutation. Transcriptomic analysis of B cell progenitors revealed key pathway alterations between Cre models such as altered IL2-Stat5 signaling pathway, differential expression of E2F targets, and altered GTPase pathway expression driven by upregulation of Guanylate Binding Proteins (GBPs) in Mx1-CreEzh2Y641Fpro-B cells. We further found that the GBP locus is regulated by Ezh2-mediated H3K27me3, it is associated with poorer survival in Acute Myeloid Leukemia patients and has variable effects on apoptosis in human lymphoma and leukemia cell lines. These findings suggest that theEzh2Y641Fmutation may alter immune regulatory pathways, cell differentiation and apoptosis, with potential implications for disease progression. Our results highlight the critical role of mutation timing and cellular context in EZH2-driven hematopoietic disease, resulting in distinct downstream changes that shape the oncogenic impact of EZH2.
Real-time volumetric imaging of cells and molecules in deep tissues with Takoyaki ultrasound
Authors: Lee Sunho , Wu Di , Malounda Dina , Rabut Claire , Shapiro Mikhail G.
Published: November 2024

Acoustic contrast agents and reporter genes play a critical role in allowing ultrasound to visualize blood flow, map molecules and track cellular function in opaque living organisms. However, existing ultrasound methods to image acoustic contrast agents predominantly focus on 2D planar imaging, while the biological phenomena of interest unfurl in three dimensions. Here, we introduce a method for efficient, dynamic imaging of contrast agents and reporter genes in 3D using multiplexed matrix array transducers. Our "Takoyaki" pulse sequence uses the simultaneous scanning of multiple focal points to excite contrast agents with sufficient acoustic pressure for nonlinear imaging while efficiently covering 3D space. Through in vitro experiments, we first show that the Takoyaki sequence produces highly sensitive volume images of gas vesicle contrast agents and compare its performance with alternative imaging schemes. We then establish its utility in cellular imaging in vivo by visualizing acoustic reporter gene-expressing tumors in a mouse model of glioblastoma. Finally, we demonstrate real-time volumetric imaging by tracking the dynamics of fluid motion in brain ventricles after intraventricular contrast injection. Takoyaki imaging enables a more comprehensive understanding of biological processes by providing spatiotemporal information in 3D within the constraints of accessible multiplexed matrix array systems.
Telomeric Repeat-Containing RNA Increases in Aged Human Cells
Authors: Hsieh Yu-Hung , Tai Chin-Hua , Yeh Meng-Ting , Chen Yu-Chen , Yang Po-Cheng , Yen Chien-Ping , Han Der-Sheng , Chu Hsueh-Ping Catherine
Published: November 2024

Telomeric repeat-containing RNA (TERRA), transcribed from subtelomeric regions towards telomeric ends, poses challenges in deciphering its complete sequences. Utilizing TERRA-capture RNA-seq and Oxford Nanopore direct RNA sequencing to acquire full-length TERRA, we annotate TERRA transcription regions in the human T2T-CHM13 reference genome. TERRA transcripts encompass hundreds to over a thousand nucleotides of telomeric repeats, predominantly originating from 61-29-37 bp repeat promoters enriched with H3K4me3, RNA pol II, CTCF, and R-loops. We develop a bioinformatics tool, TERRA-QUANT, for quantifying TERRA using RNA-seq datasets and find that TERRA increases with age in blood, brain, and fibroblasts. TERRA upregulation in aged leukocytes is confirmed by RT-qPCR. Single-cell RNA-seq analysis demonstrates TERRA expression across various cell types, with upregulation observed in neurons during human embryonic stem cell differentiation. Additionally, TERRA levels are elevated in brain cells in the early stage of Alzheimer’s disease. Our study provides evidence linking TERRA to human aging and diseases.
Benchmarking GROMACS on Optimized Colab Processors and the Flexibility of Cloud Computing for Molecular Dynamics
Authors: Karagöl Taner , Karagöl Alper
Published: November 2024

Moleculardynamics (MD) simulations are widely used computational tools in chemical and biological sciences. For these simulations, GROMACS is a popular open-source alternative among molecular dynamics simulation software designed for biochemical molecules. In addition to software, these simulations traditionally relied on costly infrastructure like supercomputers or clusters forHigh-PerformanceComputing (HPC). In recent years, there has been a significant shift towards using commercial cloud providers’ computing resources, in general. This shift is driven by the flexibility and accessibility these platforms offer, irrespective of an organization’s financial capacity. Many commercial compute platforms such asGoogleComputeEngine (GCE) andAmazonWebServices (AWS) provide scalable computing infrastructure. An alternative to these platforms is Google Colab, a cloud-based platform, provides a convenient computing solution by offering GPU and TPU resources that can be utilized for scientific computing. The accessibility of Colab makes it easier for a wider audience to conduct computational tasks without needing specialized hardware or otherwise costly infrastructure. However, running GROMACS on Colab also comes with limitations. Google Colab imposes usage restrictions, such as time limits for continuous sessions, capped at several hours, and limits on the availability of high-performance GPUs. Users may also face disruptions due to session timeouts or hardware availability constraints, which can be challenging for large or long-running molecular simulations. We have significantly enhanced the performance of GROMACS on Google Colab by re-compiling the software, compared to its default pre-compiled version. We also present a method for integrating Google Drive to save and resume interrupted simulations, ensuring that users can secure files after session-timeouts. Additionally, we detail the setup and utilization of the CUDA and MPI environment in Colab to enhance GROMACS performance. Finally, we compare the efficiency of CUDA-enabled GPUs with Google’s TPUv2 units, highlighting the trade-offs of each platform for molecular dynamics simulations. This work equips researchers, students, and educators with practical MD tools while providing insights to optimize their simulations within the Colab environment.
Finite element model of the non-keratinized buccal tissue under the impact of negative pressure
Authors: Klein Cerrejon David , Gao Daniel , Sachs David
Published: November 2024

The buccal mucosa is a highly interesting site for non-invasive drug delivery due to its relatively permeable epithelium and good accessibility. Recently, device-based systems have enabled the delivery of macromolecular drugs by leveraging mechanical stretching forces on the tissue to assist drug diffusion. Despite the successful exploitation of the buccal route with such systems, the biomechanics of buccal tissue are still poorly characterized and understood due to a lack of adequate characterization methods. Therefore, we propose a combination of physiological tissue modeling with simple suction experiments as a tool for characterizing and understanding the buccal tissue under the impact of negative pressure. Here, we present an initial step towards a multiphasic and poroelastic model specifically designed for the non-keratinized buccal tissue under the impact of negative pressure. A validated finite element model (FEM) for human skin was adapted to represent the histological structure of porcine buccal tissue. We performed suction experiments using the NIMBLE device, specifically developed for measuring skin stiffness, to characterize its mechanical behavior and train the FEM model. The resulting simulation tracks essential physiological parameters and allows the prediction of measurable changes in the tissue, such as the thinning of the epithelium and single-cell stretching. The FEM simulation was validated through histochemically stained tissue sections at the NIMBLE application site. A good correlation was demonstrated between predicted and experimentally observed changes. This work serves as a first step towards a computational representation of buccal tissue under the impact of negative pressure.
Optimization of the VSV G backbone for amino terminal fusion with nanobodies allowing its retargeting to receptors of therapeutic interest
Authors: Duquénois Isoline , Thébault Stéphanie , Johari Sarah , Raux Hélène , Ouldali Malika , Lagaudrière-Gesbert Cécile , Perez Franck , Albertini Aurélie A. , Gaudin Yves
Published: November 2024

Vesicular stomatitis virus (VSV) is a promising oncolytic virus. Additionally, its glycoprotein G is the most commonly used envelope glycoprotein to pseudotype lentiviral vectors for gene therapy. However, G receptors (LDLR family members) are ubiquitous and expressed at the surface of non-target cells, precludingin vivogene therapy. Recently, we identified G mutants that no longer bind to LDLR but retain their fusion activity. This opened the possibility of specifically retargeting the glycoprotein to receptors of interest. Here, we constructed chimeric glycoproteins fused with a nanobody at the amino-terminus of G. By experimental evolution, we identified two mutations in G improving the folding and functionality of chimeric Gs, regardless of the nanobody inserted at the amino-terminus. We then constructed chimeric glycoproteins using several nanobodies targeting HER2 receptor and, into these chimeras, we introduced mutations that abolish the recognition of LDL receptors. VSV and lentiviruses pseudotyped with these glycoproteins specifically infect cells expressing HER2. We have therefore identified G mutations that optimize the G scaffold to tolerate amino-terminal insertion of a nanobody and establish proof of concept that this approach can be used to confer a new tropism on G. This paves the way for targetedin vivotherapies.
Differential Expression Analysis with InMoose, the Integrated Multi-Omic Open-Source Environment in Python
Authors: Colange Maximilien , Appé Guillaume , Meunier Léa , Weill Solène , Nordor Akpéli , Behdenna Abdelkader
Published: November 2024

We present the differential expression features of InMoose, a Python implementation of R toolslimma, edgeR, andDESeq2. We experimentally show that InMoose stands as a drop-in replacement for those tools, with nearly identical results. This ensures reproducibility when interfacing both languages in bioinformatic pipelines. InMoose is an open source software released under the GPL3 license, available atwww.github.com/epigenelabs/inmooseandhttps://inmoose.readthedocs.io.
DistinguishingPEXgene variant severity for mild, severe, and atypical peroxisome biogenesis disorders inDrosophila
Authors: Gomez Vanessa A. , Kanca Oguz , Jangam Sharayu V. , Srivastav Saurabh , Andrews Jonathan C. , Wangler Michael F.
Published: November 2024

Peroxisomal biogenesis disorders (PBD) are autosomal recessive disorders caused by loss-of-function mutations of one of thePEXgenes responsible for peroxisomal formation. Impaired peroxisome assembly causes severe multisystemic failure with patient phenotypes ranging from epilepsy, liver disease, feeding issues, biochemical abnormalities, and neurodegeneration. Variants in the samePEXgene can produce wide differences in severity, ranging from individuals with death in the first year of life to adults with milder complications. To study this strong genotype-phenotype correlation, we selected specific humanPEXgene mutations and utilizedDrosophilaas a model organism. We generated flies replacing the coding sequence of ourPexgene of interest with aKozakGAL4 (KZ)promoter trap sequence. These cassettes simultaneously knock-out of thePexgene and knock-in aGAL4driver, ideal for making “humanized” flies in which the humanPEXgene can replace the fly loss. We assessedPex2KZandPex16KZlines in lifespan, bang sensitivity, and climbing assays and confirmed that these are strong loss-of-function alleles. In parallel, we generated human reference and variant UAS-cDNA lines ofPEX2andPEX16variants inDrosophila. We observed nearly complete phenotypic rescue ofDrosophila Pex2andPex16loss when humanPEX2ReforPEX16Ref, respectively, were expressed. We also provide evidence for an allele severity spectrum inPEX2andPEX16in which some missense alleles, such asPEX2C247R, are equally severe as early truncations, such asPEX2R119*. We also observed that alleles associated with mild PBD, such asPEX2E55K, show variability depending on the assay but do not fully rescue. Finally, alleles associated with atypical ataxia phenotypes, such asPEX16F332Del, can perform as well asPEX16Ref, depending on the assay. Altogether, theseDrosophilalines effectively model the range of severity of peroxisomal biogenesis disorders.
Steric Repulsion Counteracts ER-to-Lipid Droplet Protein Movement
Authors: Damm Alicia , Stojanović Ozren , Esch Bianca M. , Carpentier Maxime , Omrane Mohyeddine , Forêt Lionel , Fröhlich Florian , Klemm Robin , Thiam Abdou Rachid
Published: November 2024

Lipid droplets (LDs) are uniquely shaped organelles consisting of a neutral lipid core surrounded by a phospholipid monolayer, continuous with the cytosolic leaflet of the endoplasmic reticulum (ER). The dynamics and function of LDs are closely tied to their proteome composition, which is subject to dynamic remodeling. Key proteins essential for LD biology relocate from the ER to LDs, yet the mechanisms governing their movement and accumulation in LDs remain poorly understood. Here, we developed an innovative ex vivo tool to quantify and classify ER proteins based on their affinity for LDs. We found a broad spectrum of ER-to-LD partitioning affinities. We identified steric hindrance as a key factor in regulating ER-to-LD protein transfer, where proteins with only slightly higher LD affinity can effectively displace those with lower affinity from the LD surface. Consistent with this model, we observed that differentiation of 3T3 pre-adipocytes into adipocytes involves extensive remodeling of ER proteins targeting LDs, with Plin1—a high-affinity LD protein—becoming predominantly recruited and excluding other ER proteins. These findings highlight lateral protein-protein exclusion as a fundamental mechanism in shaping the LD proteome, providing new insights into LD biogenesis and function.
Amphipathic helices sense the inner nuclear membrane environment through lipid packing defects
Authors: Lee Shoken , Le Roux Anabel-Lise , Mors Mira , Vanni Stefano , Roca-Cusachs Pere , Bahmanyar Shirin
Published: November 2024

Amphipathic helices (AHs) are ubiquitous protein motifs that modulate targeting to organellar membranes by sensing differences in bulk membrane properties. However, the adaptation between membrane-targeting AHs and the nuclear membrane environment that surrounds the genome is poorly understood. Here, we computationally screened for candidate AHs in a curated list of characterized and putative human inner nuclear membrane (INM) proteins. Cell biological andin vitroexperimental assays combined with computational calculations demonstrated that AHs detect lipid packing defects over electrostatics to bind to the INM, indicating that the INM is loosely packed under basal conditions. Membrane tension resulting from hypotonic shock further promoted AH binding to the INM, whereas cell-substrate stretch did not enhance recruitment of membrane tension-sensitive AHs. Together, our work demonstrates the rules driving lipid-protein interactions at the INM, and its implications in the response of the nucleus to different stimuli.
The effects of soleus push up on glucose tolerance among individuals with prediabetes
Authors: Elek Dávid , Tóth Miklós , Sonkodi Balázs , Ács Pongrác , Kovács Gábor L. , Melczer Csaba
Published: November 2024

The objective of this study was to assess the efficacy of a previously invented soleus-dominant exercise in reducing postprandial blood glucose levels in individuals with prediabetes and to evaluate the feasibility of incorporating this soleus push up exercise into their daily routine. It seems that performing the mostly soleus-involved activity in a sitting position during the oral glucose tolerance test results in ∼32% lower postprandial glucose excursion than the control results. This effect is also present in the absence of electromyographic feedback. Hereby we conclude that performing this repetitive prolonged contractile muscle activity may help metabolic regulation even in prediabetic people without the need of a laboratory setting. Therefore soleus push up is a potent exercise method that can be effectively completed in a home setting or work environment. However, further validation of this treatment method should be studied in a larger sample size.