bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell genotype-phenotype mapping identifies therapeutic vulnerabilities in VEXAS syndrome
Authors: Ganesan Saravanan , Murray Rebecca M. , Sotelo Jesus , Eton Elliot O. , Takashima Kouhei , Botella Theo , Beattie Kai , Indart Alyssa C. , Chraiki Nada , Croizier Carolyne , Izzo Franco , Potenski Catherine , Marro Samuele , Wu Zhijie , Gao Shouguo , Young Neal S. , Blair John D. , Satija Rahul , Terrier Benjamin , Heiblig Mael , Raimondi Ivan , Papapetrou Eirini P , Sujobert Pierre , Kosmider Olivier , Beck David B. , Landau Dan A. 
Published: May 2024

AbstractSomatic evolution leads to the emergence of clonal diversity across tissues with broad implications for human health. A striking example of somatic evolution is the VEXAS (Vacuoles E1 enzyme X-linked Autoinflammatory Somatic) syndrome, caused by somaticUBA1mutations in hematopoietic stem cells (HSCs), inducing treatment-refractory, systemic inflammation. However, the mechanisms that lead to survival and expansion of mutant HSCs are unknown, limiting the development of effective therapies. The lack of animal or cellular models ofUBA1-mutant HSCs has hindered such mechanistic understanding, mandating analysis of primary human VEXAS samples, which harbor admixtures of wild-type andUBA1-mutant HSCs. To address these challenges, we applied single-cell multi-omics to comprehensively define mutantUBA1-induced transcriptome, chromatin accessibility and signaling pathway alterations in VEXAS patients, allowing for the direct comparison of mutant versus wild-type cells within the same environment. We confirmed the expected enrichment ofUBA1M41V/Tmutations in myeloid cells, and additionally discovered that these mutations were also prevalent in Natural Killer (NK) cells in VEXAS patients, providing new insights into disease phenotypes. Through mapping genotypes to molecular phenotypes, including transcriptome, chromatin accessibility, cell surface protein or intracellular protein profiles, in HSCs, we found thatUBA1M41V/T-mutant cells showed an increased inflammation signature (interferon alpha and gamma response pathways), as well as activation of unfolded protein response (UPR) via pro-survival, but not pro-apoptotic, mediators of the PERK pathway, compared toUBA1wild-type HSCs. Ex vivo validation experiments showed that inhibitingUBA1in normal CD34+ or usingUBA1-mutant HSCs led to PERK pathway up-regulation, increased myeloid differentiation and cell survival, which was reversed by PERK inhibition. Thus, we demonstrated that human VEXAS HSCs show cell-intrinsic inflammatory phenotypes and survive the proteomic stress caused by compromised ubiquitination through PERK-mediated activation of the UPR. Together, these analyses nominate PERK pathway inhibition as a potential new therapeutic strategy for eradicating the VEXAS-inducing clone, demonstrating the power of single-cell multi-omics profiling of primary patient sample to enable genotype-to-phenotype somatic mapping for the discovery of novel candidates for clinical intervention.
Short-term Electrical Stimulation Impacts Cardiac Cell Structure and Function
Authors: Allen Kristen , Bandl Abigail , Pachter Natalie , Hookway Tracy 
Published: May 2024

AbstractInduced pluripotent stem cell derived cardiomyocytes (iPSC-CMs) are used to model cardiac development and disease. This requires a robust population of mature CMs and external stimuli to mimic the complex environment of the heart. In effort toward this maturation, previous groups have applied electrical stimulation (ES) to CMs with varying results depending on the stimulation duration, frequency, and pattern. As such, there is uncertainty surrounding the timeline on which stimulated iPSC-CMs begin to show early signs of maturation in comparison to their non-stimulated counterparts, leaving room for additional research into when hallmarks of maturity–such as hypertrophy and changes to sarcomere structure–develop in CMs. Here, we introduce a low-cost custom bioreactor capable of delivering tunable electrical stimulation to standard 2D cell monolayers. We show that, after exposure to short-term ES, stimulated CMs express early signs of maturation compared to the non-stimulated control. The changes to contractility and protein expression indicate that the cells undergo hypertrophy in response to short-term ES, but they do not develop transverse-tubules, which is a key component of a fully mature CM structure. Therefore, while early signs of maturation are present after a short stimulation regimen, additional cellular structures must develop to reach complete maturation. We have shown that our custom electrical stimulator can be easily integrated with standardin vitrocell culture platforms to obtain measurable changes to cells, exhibiting its potential for promoting crucial CM maturation for cardiac tissue engineering applications.
iResNetDM: interpretable and comprehensive deep learning model for 4 types of DNA modifications prediction
Authors: Yang Zerui , Shao Wei , Matsuda Yudai , Song Linqi 
Published: May 2024

AbstractMotivationDespite the development of several computational methods to predict DNA modifications, two main limitations persist in the current methodologies: 1) All existing models are confined to binary predictor which merely determine the presence or absence of DNA modifications, constraining comprehensive analyses of the interrelations among varied modification types. While multi-class classification models for RNA modifications have been developed, a comparable approach for DNA remains a critical need. 2) The majority of previous studies lack adequate explanations of how models make decisions, relying on the extraction and visualization of attention matrices which identified few motifs, and do not provide sufficient insight into the model decision making process.ResultIn this study, we introduce iResNetDM, a deep learning model that integrates ResNet and self-attention mechanisms. To the best of our knowledge, iResNetDM is the first model capable of distinguishing between four types of DNA modifications. It not only demonstrates high performance across various DNA modifications but also unveils the potential capabilities of CNN and ResNet in this domain. To augment the interpretability of our model, we implemented the integrated gradients technique, which was pivotal in demystifying the model’s decision-making framework, allowing for the successful identification of multiple motifs. Importantly, our model exhibits remarkable robustness, successfully identifying unique motifs across different modifications. Furthermore, we compared the motifs discovered in various modifications, revealing that some motifs share significant sequence similarities which suggests that these motifs may be subjected to different types of modifications, underscoring their potential importance in gene regulation.Contactzeruiyang2-c@my.cityu.edu.hk
A Data-Intelligence-Intensive Bioinformatics Copilot System for Large-scale Omics Researches and Scientific Insights
Authors: Liu Yang , Shen Rongbo , Zhou Lu , Xiao Qingyu , Yuan Jiao , Li Yixue 
Published: May 2024

AbstractAdvancements in high-throughput sequencing technologies and artificial intelligence offer unprecedented opportunities for groundbreaking discoveries in bioinformatics research. However, the challenges of exponential growth of omics data and the rapid development of artificial intelligence technologies require automated big biological data analysis capability and interdisciplinary knowledge-driven scientific insight. Here we propose a data-intelligence-intensive bioinformatics copilot (Bio-Copilot) system that synergizes AI capabilities with human expertise to facilitate hypothesis-free exploratory research and inspire novel scientific insights in large-scale omics studies. Bio-Copilot forms high-quality intensive intelligence through close collaboration between multiple agents, driven by large language models (LLMs), and human experts. To augment the capabilities of Bio-Copilot, this study devises an agent group management strategy, an effective human-agent interaction mechanism, a shared interdisciplinary knowledge database, and continuous learning strategies for the agents. We comprehensively compare Bio-Copilot against GPT-4o and several leading AI agents across diverse bioinformatics tasks, using a broad range of evaluation metrics. Bio-Copilot achieves the overall state-of-the-art performance across all tasks, while showcases exceptional task completeness. Furthermore, in the application of constructing a large-scale human lung cell atlas, Bio-Copilot not only reproduces the intricate data integration process detailed in a seminal study but also introduces a hierarchical annotation strategy to capture the continuous nature of cellular states and uncovers the characteristics of rare cell types, highlighting its potential to unravel hidden complexities in biological systems. Beyond the technical achievements, this study also underscores the profound implications of integrating AI capabilities with expert knowledge in accelerating impactful biological discoveries and exploring uncharted territories in life sciences.
Production of four-gene (GTKO/hCD55/hTBM/hCD39)-edited donor pigs and kidney xenotransplantation
Authors: Yang Chang , Wei Yunfang , Li Xinglong , Xu Kaixiang , Huo Xiaoying , Chen Gang , Zhao Heng , Wang Jiaoxiang , Wei Taiyun , Qing Yubo , Guo Jianxiong , Zhao Hongfang , Zhang Xiong , Jiao Deling , Xiong Zhe , Jamal Muhammad Ameen , Zhao Hong-Ye , Wei Hong-Jiang 
Published: May 2024

AbstractBackgroundThe number of multigene-modified donor pigs for xenotransplantation is increasing with the advent of gene editing technologies. However, which gene combination is suitable for which organ transplantation remains unclear.MethodsIn this study, we utilized CRISPR/Cas9 gene editing technology, PiggyBac transposon system and somatic cell cloning to construct GTKO/hCD55/hTBM/hCD39 four-gene-edited cloned (GEC) pigs and performed kidney transplantation from pig to rhesus monkey to evaluate the effectiveness of these GEC pigs.ResultsFirst, 107 cell colonies were obtained through drug selection, of which 7 were 4-GE colonies. Two colonies were selected for somatic cell nuclear transfer, resulting in 7 fetuses, of which 4 were GGTA1 biallelic knockout. Both fetuses had higher expression of hCD55, hTBM and hCD39. Therefore, these two fetuses were selected for two consecutive rounds of cloning, resulting in a total of 97 live piglets. After phenotype identification, the GGTA1 gene of these pigs was inactivated, and hCD55, hTBM and hCD39 were expressed in cells and multiple tissues. Furthermore, the numbers of monkey IgM and IgG binding to the peripheral blood mononuclear cells (PBMCs) of the 4-GEC pigs were markedly reduced. Moreover, 4-GEC porcine PBMCs had greater survival rates than those from wild-type pigs through complement-mediated cytolysis assays. In pig-to-monkey kidney xenotransplantation, the kidney xenograft successfully survived for 11 days. All physiological and biochemical indicators were normal, and no hyperacute rejection or coagulation abnormalities were found after transplantation.ConclusionThese results indicate that the GTKO/hCD55/hTBM/hCD39 four-gene modification effectively alleviates immune rejection, and the pig kidney can functionally support the recipient monkey’s life.
Seclidemstat blocks the transcriptional function of multiple FET-fusion oncoproteins
Authors: Rask Galen C. , Taslim Cenny , Bayanjargal Ariunaa , Cannon Matthew V. , Selich-Anderson Julia , Crow Jesse C. , Duncan Aundrietta , Theisen Emily R. 
Published: May 2024

ABSTRACTGenes encoding the RNA-binding proteinsFUS,EWSR1, andTAF15 (FET proteins) are involved in chromosomal translocations in rare sarcomas. FET-rearranged sarcomas are often aggressive malignancies affecting patients of all ages. New therapies are needed. These translocations fuse the 5’ portion of the FET gene with a 3’ partner gene encoding a transcription factor (TF). The resulting fusion proteins are oncogenic TFs with a FET protein low complexity domain (LCD) and a DNA binding domain. FET fusion proteins have proven stubbornly difficult to target directly and promising strategies target critical co-regulators. One candidate is lysine specific demethylase 1 (LSD1). LSD1 is recruited by multiple FET fusions, including EWSR1::FLI1. LSD1 promotes EWSR1::FLI1 activity and treatment with the noncompetitive inhibitor SP-2509 blocks EWSR1::FLI1 transcriptional function. A similar molecule, seclidemstat (SP-2577), is currently in clinical trials for FET-rearranged sarcomas (NCT03600649). However, whether seclidemstat has pharmacological activity against FET fusions has not been demonstrated. Here, we evaluate thein vitropotency of seclidemstat against multiple FET-rearranged sarcoma cell lines, including Ewing sarcoma, desmoplastic small round cell tumor, clear cell sarcoma, and myxoid liposarcoma. We also define the transcriptomic effects of seclidemstat treatment and evaluated the activity of seclidemstat against FET fusion transcriptional regulation. Seclidemstat showed potent activity in cell viability assays across FET-rearranged sarcomas and disrupted the transcriptional function of all tested fusions. Though epigenetic and targeted inhibitors are unlikely to be effective as a single agents in the clinic, these data suggest seclidemstat remains a promising new treatment strategy for patients with FET-rearranged sarcomas.SIGNIFICANCEHere, we show the noncompetitive inhibitor, seclidemstat, hasin vitroactivity against multiple FET fusion proteins that cause a number of rare and aggressive sarcomas. These data represent one of the largest analyses of FET fusion activity across multiple malignancies and are a valuable resource for those studying FET-rearranged sarcomas.
Transfer Elastic Net for Developing Epigenetic Clocks for the Japanese Population
Authors: Tomo Yui , Nakaki Ryo 
Published: May 2024

AbstractMotivationThe epigenetic clock evaluates human biological age based on DNA methylation patterns. It takes the form of a regression model where the methylation ratio at CpG sites serves as the predictor, and chronological or adjusted age as the response variable. Due to the large number of CpG sites considered as candidate explanatory variables and their potential correlation, Elastic Net is commonly used to train the regression models. However, existing standard epigenetic clocks, trained on multiracial data, may exhibit biases due to genetic and environmental differences among specific racial groups. The development of epigenetic clocks suitable for a single-race population typically necessitates the collection of hundreds to thousands of samples to measure DNA methylation and other biomarkers, which costs a lot of time and money. Consequently, a method for developing accurate epigenetic clocks with relatively small sample sizes is needed.ResultsWe propose Transfer Elastic Net, a transfer learning approach that uses the parameter information from a linear regression model trained with the Elastic Net to estimate another model. Using this method, we constructed Horvath’s, Hannum’s, and Levine’s types of epigenetic clocks using DNA methylation data from blood samples of 143 Japanese subjects. The data were transformed through principal component analysis to obtain more reliable clocks. The developed clocks demonstrated the smallest prediction errors compared to both the original clocks and those trained with the Elastic Net on the same Japanese data. Furthermore, the bias relative to the original clocks was reduced. Thus, we successfully developed epigenetic clocks that are well-suited for the Japanese population. Transfer Elastic Net can also be applied to develop epigenetic clocks for other specific populations, and is expected to be applied in various fields.Availabilityhttps://github.com/t-yui/TransferENet-EpigeneticClock
A nitrogenase-like enzyme is involved in the novel anaerobic assimilation pathway of a sulfonate, isethionate, in the photosynthetic bacteriumRhodobacter capsulatus
Authors: Morimoto Yoshiki , Uesaka Kazuma , Fujita Yuichi , Yamamoto Haruki 
Published: May 2024

SummaryProkaryotes contribute to the global sulfur cycle by using diverse sulfur compounds as sulfur sources or electron acceptors. Here we report that a nitrogenase-like enzyme (NFL) and a radical SAM enzyme (RSE) are involved in the novel anaerobic assimilation pathway of a sulfonate, isethionate, in the photosynthetic bacteriumRhodobacter capsulatus. ThenflHDKgenes for NFL are localized at a locus containing genes for known sulfonate metabolism in the genome. A genenflBencoding an RSE is present just upstream ofnflH, forming a small gene clusternflBHDK. Mutants lacking anynflBHDKgenes lost the ability to grow with isethionate as the sole sulfur source under anaerobic photosynthetic conditions, indicating that all four NflBHDK proteins are essential for the isethionate assimilation pathway. Heterologous expression of theislABgenes encoding a known isethionate lyase that degrades isethionate to sulfite and acetaldehyde restored the isethionate-dependent growth of a mutant lackingnflDK, indicating that the enzyme encodingnflBHDKis involved in an isethionate assimilation reaction to release sulfite. Furthermore, heterologous expression ofnflBHDKandssuCABencoding an isethionate transporter in the closely related speciesR. sphaeroides, which does not havenflBHDKand cannot grow with isethionate as the sole sulfur source, conferred isethionate-dependent growth ability to this species. We propose to renamenflBHDKasisrBHDK(isethionate reductase). TheisrBHDKgenes are widely distributed among various prokaryote phyla. Discovery of the isethionate assimilation pathway by IsrBHDK provides a missing piece for the anaerobic sulfur cycle and for understanding the evolution of ancient sulfur metabolism.ImportanceNitrogenase is an important enzyme found in prokaryotes that reduces atmospheric nitrogen to ammonia and plays a fundamental role in the global nitrogen cycle. It has been noted that nitrogenase-like enzymes (NFLs), which share an evolutionary origin with nitrogenase, have evolved to catalyze diverse reactions such as chlorophyll biosynthesis (photosynthesis), coenzyme F430biosynthesis (methanogenesis), and methionine biosynthesis. In this study, we discovered that an NFL with unknown function in the photosynthetic bacteriumRhodobacter capsulatusis a novel isethionate reductase (Isr), which catalyzes the assimilatory degradation of isethionate, a sulfonate, releasing sulfite used as the sulfur source under anaerobic conditions. Isr is widely distributed among various bacterial phyla, including intestinal bacteria, and is presumed to play an important role in sulfur metabolism in anaerobic environments such as animal guts and microbial mats. This finding provides a clue for understanding ancient metabolism that evolved under anaerobic environments at the dawn of life.
Isolation and characterization of three lytic podo-bacteriophages with two receptor recognition modules against multidrug-resistantKlebsiella pneumoniae
Authors: Huang Liang , Huang Xueting , Zhao Tongfei , Zhang Jingren , Xiang Ye 
Published: May 2024

AbstractThe multidrug-resistant nosocomial pathogenKlebsiella pneumoniaeis considered as one of the major threats to public health. Recent studies showed that bacteriophages could be used as an alternative to antibiotics for treating infections caused by multidrug-resistantK. pneumoniae.Here we isolated and characterized three lytic bacteriophages Kp7, Kp9 and Kp11 ofK. pneumoniae. Transmission electron microscopy analysis showed that all three phages have an isometric head of approximately 60 nm in diameter and a short noncontractile tail. Host specificity, one-step growth curve, tolerance to pH and temperature changes were characterized for Kp7, Kp9, and Kp11. Mass-spectrum and bioinformatical analysis identified two different types of tail fibers in each phage. The tail fiber proteins gp52 of Kp7, gp43 of Kp9 and gp46 of Kp11 are homologous and have robust enzymatic activity in digesting purified serotype K2 capsule ofK. pneumoniae. However, tail fiber proteins gp51 of Kp7, gp42 of Kp9 and gp45 of Kp11 have diverse sequences and show weak or no enzyme activity in digesting purified serotype K2 capsule. Genetic knockout and biochemical assays indicated that the capsule is essential for the infection of Kp7, Kp9 and Kp11. Spot tests showed that 15 clinical isolates of drug-resistantK. pneumoniaewith the serotype K2 capsule can all be infected by Kp7, Kp9 and Kp11 but with different susceptibility. Further mechanistic studies showed that transcriptional inhibition at the early stage of phage infection determines the susceptibility of differentK. pneumoniaeisolates.
Seizures may worsen outcomes of neonatal hypoxic ischemic encephalopathy: a longitudinal serum biomarkers study
Authors: Aziz Khyzer B , Kuiper Jordan , Kilborn Alison , Kambli Hrishikesh , Jayakumar Srishti , Gerner Gwendolyn J , Tekes Aylin , Parkinson Charlamaine , Graham Ernest M. , Stafstrom Carl E. , Campbell Christopher , Demos Catherine , Stengelin Martin , Sigal George , Wohlstadter Jacob , Everett Allen D. , Northington Frances J. , Chavez-Valdez Raul 
Published: May 2024

ABSTRACTIntroductionScreening and treatment of seizures (Sz) in neonates suffering from hypoxic-ischemic encephalopathy (HIE) is routine. Understanding if Sz worsen brain injury and outcomes would optimize treatment decisions, recognizing risks and benefits. We hypothesized that serum central nervous system (CNS)-specific biomarkers would discriminate neonates with Sz and relate to outcomes.MethodsThis retrospective cohort study was conducted between April 28, 2009 and November 15, 2019, including neonates diagnosed with seizures (Sz) and/or HIE treated with therapeutic hypothermia (TH), who had sufficient remnant serum for biomarker analysis. Neonates were grouped in i) only Sz without HIE (Sz-no HIE), ii) HIE with Sz (Sz-HIE) and iii) HIE without Sz (no Sz-HIE). Levels of glial fibrillary acidic protein (GFAP, astrocytic reactivity), Tau (neuronal injury) and neurofilament light chain (NF-L, axonal degeneration) were studied at admission, <72h and 72-144h of life against time to full oral feeds and brain injury in MRI.ResultsAfter exclusions 145 neonates were included (61% male; 33% Black). Admission GFAP levels were higher in Sz-HIE than in no Sz-HIE neonates. During the first 72h of life, levels of all 3 biomarkers were similar between Sz groups (Sz-no HIE & Sz-HIE), but higher than in no Sz-HIE. After 72h, NF-L and Tau remained higher in both Sz groups vs. no Sz-HIE. Stroke diagnosed in 31% (Sz-no HIE), 8% (Sz-HIE) and 11% (no Sz-HIE) of neonates had no effect in biomarkers levels. In adjusted regression models higher Tau and NF-L percentiles related to longer time to reach full oral feeding and higher odds of significant brain injury in MRI in both Sz groups.ConclusionsIn this study, Tau and NF-L levels are higher in those neonates developing Sz, irrespective of their HIE diagnosis. These results provide additional support for the notion that Sz may worsen brain injury and outcomes in neonates with HIE even with TH.