bluuebunny/crossref_metadata_2025_split huggingface dataset:
A lineage-resolved multimodal single-cell atlas reveals the genomic dynamics of earlyC. elegansdevelopment
Authors: van der Burght Servaas N. , Carelli Francesco N. , Appert Alex , Dong Yan , Hill Matthew , Buttress Toby , Butler Richard , Ahringer Julie 
Published: December 2024

AbstractMultimodal single-cell profiling provides a powerful approach for unravelling the gene regulatory mechanisms that drive development, by simultaneously capturing cell-type- specific transcriptional and chromatin states. However, its inherently destructive nature hampers the ability to trace regulatory dynamics between mother and daughter cells. Taking advantage of the invariant cell lineage of Caenorhabditis elegans, we constructed a lineage- resolved single-cell multimodal map of pre-gastrulation development, which allows the tracing of chromatin and gene expression changes across cell divisions and regulatory cascades. We characterise the early dynamics of genome regulation, revealing that zygotic genome activation occurs on an accessible chromatin landscape pre-patterned both maternally and zygotically, and we identify a redundant family of transcriptional regulators that drive a transient pre-gastrulation program. Our findings demonstrate the power of a lineage-resolved atlas for dissecting the genome regulatory events of development.
Downregulation of Gankyrin/PSMD10 affects cancer cell growth and proliferation in glioblastoma:in vitroandin vivostudy
Authors: Travnikova Daria , Shashkovskaya Vera , Kordyukova Maria , Nosova Irina , Kudryashova Olga , Zatsepin Timofei , Belousov Vsevolod , Abakumova Tatiana 
Published: December 2024

AbstractThe oncoprotein Gankyrin/PSMD10 is upregulated in various cancers, including glioblastoma multiforme (GBM), the most difficult tumor to treat. The heterogeneity of this type of tumor requires a multi-targeted approach to overcome radio- and chemoresistance. Here we aim to investigate the effects of Gankyrin inhibition on glioma cell proliferation and its impact on sensitivity to chemotherapy bothin vitroandin vivo. We have employed the RNA interference approach as a valuable tool to downregulate the expression of target genes. Small interfering RNA (siRNA) were formulated into lipid nanoparticles (LNP) to facilitate delivery and overcome challenges, including RNase activity. We demonstrate that knockdown of Gankyrin promotes cell growth arrest of murine (GL261, CT-2А) and human (U87, GBM23, GBM24) glioma cells and induces the generation of reactive oxygen species and apoptosis. Importantly, Gankyrin inhibition enhances the therapeutic effect of temozolomide in murine glioma cell lines and decreases the IC50 of doxorubicin and cisplatin for U87 and GL261 cells. The therapeutic potential of Gankyrin inhibition was shown in patient-derived glioblastoma stem cells, which are responsible for tumor initiation and resistance to therapy. We showed that downregulation of Gankyrin led to decreased cell proliferationin vitroand improved survival in xenograft glioma model mice. Our results suggest that harnessing siRNA against Gankyrin may serve as a novel therapeutic strategy for glioblastoma therapy in a multi-drug approach and address challenges in current treatment by sensitizing glioma cells to chemotherapy.HighlightssiRNA-mediated knockdown of Gankyrin reduced cell proliferation of murine and human glioma cells, induced ROS generation and promoted apoptosis.Inhibition of Gankyrin increased the therapeutic effect of temozolomide in resistant CT- 2A glioma cells and decreased the IC50 concentration of doxorubicin and cisplatin in U87 and GL261 cells.Downregulation of Gankyrin inhibited the growth of patient-derived glioma stem cells and increased the survival of NOD/SCID xenograft glioma model mice
CoLaML: Inferring latent evolutionary modes from heterogeneous gene content
Authors: Yamanouchi Shun , Fukunaga Tsukasa , Iwasaki Wataru 
Published: December 2024

ABSTRACTMotivationEstimating the history of gene content evolution provides insights into genome evolution on a macroevolutionary timescale. Previous models did not consider heterogeneity in evolutionary patterns among gene families across different periods and/or clades.ResultsWe introduce CoLaML (joint inference of gene COntent evolution and its LA-tent modes using Maximum Likelihood), which considers heterogeneity using a Markov-modulated Markov chain. This model assumes that internal states determine evolutionary patterns (i.e., latent evolutionary modes) and attributes heterogeneity to their switchover during the evolutionary timeline. We developed a practical algorithm for model inference and validated its performance through simulations. CoLaML outperformed previous models in fitting empirical datasets and estimated plausible evolutionary histories, capturing heterogeneity among clades and gene families without prior knowledge.AvailabilityCoLaML is freely available athttps://github.com/mtnouchi/colaml.Contactyamanouchi@bs.s.u-tokyo.ac.jp
Target cell tension regulates macrophage trogocytosis
Authors: Cornell Caitlin E. , Chorlay Aymeric , Krishnamurthy Deepak , Martin Nicholas R. , Baldauf Lucia , Fletcher Daniel A. 
Published: December 2024

SummaryMacrophages are known to engulf small membrane fragments, or trogocytose, target cells and pathogens, rather than fully phagocytose them. However, little is known about what causes macrophages to choose trogocytosis versus phagocytosis. Here, we report that cortical tension of target cells is a key regulator of macrophage trogocytosis. At low tension, macrophages will preferentially trogocytose antibody-opsonized cells, while at high tension they tend towards phagocytosis. Using model vesicles, we demonstrate that macrophages will rapidly switch from trogocytosis to phagocytosis when membrane tension is increased. Stiffening the cortex of target cells also biases macrophages to phagocytose them, a trend that can be countered by increasing antibody surface density and is captured in a mechanical model of trogocytosis. This work suggests that a distinct molecular pathway for trogocytosis is not required to explain differences in trogocytosis among target cell types and points to a mechanism for target cells to modulate trogocytosis.
Genomic network analysis characterizes genetic architecture and identifies trait-specific biology
Authors: Thorp Jackson G. , Gerring Zachary F. , Reay William R. , Derks Eske M. , Grotzinger Andrew D. 
Published: December 2024

AbstractPervasive genetic overlap across human complex traits necessitates developing multivariate methods that can parse pleiotropic and trait-specific genetic signals. Here, we introduce Genomic Network Analysis (GNA), an analytic framework that applies the principles of network modelling to estimates of genetic overlap derived from genome-wide association study (GWAS) summary statistics. The result is a genomic network that describes the conditionally independent genetic associations between traits that remain when controlling for shared signal with the broader network of traits. Graph theory metrics provide added insight by formally quantifying the most important traits in the genomic network. GNA can discover additional trait-specific pathways by incorporating gene expression or genetic variants into the network to estimate their conditional associations with each trait. Extensive simulations establish GNA is well-powered for most GWAS. Application to a diverse set of traits demonstrate that GNA yields critical insight into the genetic architecture that demarcate genetically overlapping traits at varying levels of biological granularity.
Autoimmune side-effect of immunotherapy in lung cancer treatment revealed from large-scale cohort
Authors: Sun Yan , Yang Shihao 
Published: December 2024

AbstractAlthough immune checkpoint inhibitors have illustrated strong benefits in patient survival and have been widely acknowledged in treating lung cancer, they may be subject to increased risk of immune-related adverse effects (irAEs). Although existing literature have studied the mechanisms of irAEs of immunotherapy, it is difficult to quantify such effect, especially at a large-scale real-world population level. In this paper, the autoimmune-related risk of multiple immune checkpoint inhibitors is compared with that of chemotherapy based on Medicaid and CHIP TAF (T-MSIS Analytic File) data of over 100,000 patient samples from 2012 to 2018. Results show that the irAEs of immunotherapy is significantly higher than chemotherapy in both unadjusted and adjusted samples from the dataset. Analysis on subpopulation and specific disease types further shows that certain immunotherapy treatments are associated with higher risk of irAEs, and the risk of certain autoimmune diseases may vary. We also illustrate the robustness of our conclusion through additional sensitivity analysis, confirming the necessity of keeping track of autoimmune side effects of immune checkpoint inhibitors for medicine researchers. Our methods are also available to evaluate effectiveness and side effects of novel therapies at a large-scale population level.
The oncogene SLC35F2 is a high-specificity transporter for the micronutrients queuine and queuosine
Authors: Burtnyak Lyubomyr , Yuan Yifeng , Pan Xiaobei , Gunaratne Lankani , d’Almeida Gabriel Silveira , Martinelli Maria , Reed Colbie , Garcia Jessie Fernandez , Patel Bhargesh Indravadan , Marquez Isaac , Ehrenhofer-Murray Ann E. , Swairjo Manal A. , Alfonzo Juan D. , Green Brian D. , Kelly Vincent P. , de Crécy-Lagard Valérie 
Published: December 2024

AbstractThe nucleobase queuine (q) and its nucleoside queuosine (Q) are micronutrients derived from bacteria that are acquired from the gut microbiome and/or diet in humans. Following cellular uptake, Q is incorporated at the wobble base (position 34) of tRNAs with a GUN anticodon, which is important for efficient translation. Early studies suggested that cytosolic uptake of queuine is mediated by a selective transporter that is regulated by mitogenic signals, but the identity of this transporter has remained elusive. Here, through a cross-species bioinformatic search and genetic validation, we have identified the solute carrier family member SLC35F2 as a unique transporter for both queuine and queuosine inSchizosaccharomyces pombeandTrypanosoma brucei. Furthermore, gene disruption in HeLa cells revealed that SLC35F2 is the sole transporter for queuosine in HeLa cells (Km174 nM) and a high-affinity transporter for the queuine nucleobase (Km67 nM), with the presence of another low-affinity transporter (Km259 nM) in these cells. Competition uptake studies show that SLC35F2 is not a general transporter for other canonical ribonucleobases or ribonucleosides, but selectively imports q and Q. The identification of SLC35F2, an oncogene, as the transporter of both q and Q advances our understanding of how intracellular levels of queuine and queuosine are regulated and how their deficiency contributes to a variety of pathophysiological conditions, including neurological disorders and cancer.Significance StatementThe discovery of SLC35F2 as the eukaryotic transporter of queuine and queuosine is key to understanding how these micronutrients are salvaged from the human gut and distributed to different body tissues. Queuosine modification of tRNAs enhances the accuracy and efficiency of codon-anticodon pairing and regulates a range of biological and pathophysiological states, including oxidative stress responses, cancer, learning, memory, and gut homeostasis.
Remission spectroscopy resolves the mode of action of bedaquiline within living mycobacteria
Authors: Harrison Suzanna H , Walters Rowan C , Cheung Chen-Yi , Springett Roger J , Cook Gregory M , Osman Morwan M , Blaza James N 
Published: December 2024

AbstractBedaquiline, an ATP synthase inhibitor, is the spearhead of transformative therapies against drug-resistantMycobacterium tuberculosis. Beyond causing a cellular energetic crisis, differentin vivomechanisms of action have been proposed. Here, we apply remission spectroscopy to measure the electron-occupancy of the energy-transducing cytochromes within the mycobacterial and human bioenergetic systems as they power living cells. We find no evidence for bedaquiline’s protonophoric or ionophoric uncoupling activity but observe sub-second redirection of electron flux to the cytochromebdoxidase, Cyd, bypassing the respiratory control ATP synthase imposes on the electron transport chain. We find that bedaquiline does not affect human mitochondrial function. Overall, we explain how bedaquiline works, why different models for its action developed, and the mechanisms underlying bedaquiline’s synergy in combination regimes.
Cardiac Applications of CRISPR/AAV-Mediated Precise Genome Editing
Authors: Zheng Yanjiang , Mayourian Joshua , King Justin S. , Li Yifei , Bezzerides Vassilios J. , Pu William T. , VanDusen Nathan J. 
Published: December 2024

AbstractThe ability to efficiently make precise genome edits in somatic tissues will have profound implications for gene therapy and basic science. CRISPR/Cas9 mediated homology-directed repair (HDR) is one approach that is commonly used to achieve precise and efficient editing in cultured cells. Previously, we developed a platform capable of delivering CRISPR/Cas9 gRNAs and donor templates viaadeno-associatedvirus to induceHDR(CASAAV-HDR). We demonstrated that CASAAV-HDR is capable of creating precise genome editsin vivowithin mouse cardiomyocytes at the neonatal and adult stages. Here, we report several applications of CASAAV-HDR in cardiomyocytes. First, we show the utility of CASAAV-HDR for disease modeling applications by using CASAAV-HDR to create and precisely tag two pathological variants of the titin gene observed in cardiomyopathy patients. We used this approach to monitor the cellular localization of the variants, resulting in mechanistic insights into their pathological functions. Next, we utilized CASAAV-HDR to create another mutation associated with human cardiomyopathy, arginine 14 deletion (R14Del) within the N-terminus of Phospholamban (PLN). We assessed the localization of PLN-R14Del and quantified cardiomyocyte phenotypes associated with cardiomyopathy, including cell morphology, activation of PLN via phosphorylation, and calcium handling. After demonstrating CASAAV-HDR utility for disease modeling we next tested its utility for functional genomics, by targeted genomic insertion of a library of enhancers for a massively parallel reporter assay (MPRA). We show that MPRAs with genomically integrated enhancers are feasible, and can yield superior assay sensitivity compared to tests of the same enhancers in an AAV/episomal context. Collectively, our study showcases multiple applications forin vivoprecise editing of cardiomyocyte genomes via CASAAV-HDR.
Conservation of function without conservation of amino acid sequence in intrinsically disordered transcriptional activation domains
Authors: LeBlanc Claire , Stefani Jordan , Soriano Melvin , Lam Angelica , Zintel Marissa A. , Kotha Sanjana R. , Chase Emily , Pimentel-Solorio Giovani , Vunnum Aditya , Flug Katherine , Fultineer Aaron , Hummel Niklas , Staller Max V. 
Published: December 2024

AbstractProtein function is canonically believed to be more conserved than amino acid sequence, but this idea is only well supported in folded domains, where highly diverged sequences can fold into equivalent 3D structures. In contrast, intrinsically disordered protein regions (IDRs) do not fold into a stable 3D structure, thus it remains unknown when and how function is conserved for IDRs that experience rapid amino acid sequence divergence. As a model system for studying the evolution of IDRs, we examined transcriptional activation domains, the regions of transcription factors that bind to coactivator complexes. We systematically identified activation domains on 502 orthologs of the transcriptional activator Gcn4 spanning 600 MY of fungal evolution. We find that the central activation domain shows strong conservation of function without conservation of sequence. This conservation of function without conservation of sequence is facilitated by evolutionary turnover (gain and loss) of key acidic and aromatic residues, the positions most important for function. This high sequence flexibility of functional orthologs mirrors the physical flexibility of the activation domain coactivator interaction interface, suggesting that physical flexibility enables evolutionary plasticity. We propose that turnover of short functional elements, sometimes individual amino acids, is a general mechanism for conservation of function without conservation of sequence during IDR evolution.
Lineage–specific amino acids define functional attributes of the protomer-protomer interfaces for the Rad51 and Dmc1 recombinases
Authors: Petassi Mike , Shin Yeonoh , Jessop Aidan M. , Morse Katherine , Kim Stefan Y. , Matei Razvan , Raina Vivek B. , Greene Eric C. 
Published: December 2024

ABSTRACTMost eukaryotes possess two Rad51/RecA family DNA recombinases that are thought to have arisen from an ancient gene duplication event: Rad51, which is expressed in both mitosis and meiosis; and Dmc1, which is only expressed in meiosis. To explore the evolutionary relationship between these recombinases, here, we present high-resolution CryoEM structures ofS. cerevisiaeRad51 filaments andS. cerevisiaeDmc1 filaments bound to ssDNA, which reveal a pair of stacked interfacial aromatic amino acid residues that are nearly universally conserved in Rad51 but are absent from Dmc1. We use a combination of bioinformatics, genetic analysis of natural sequence variation, and deep mutational analysis to probe the functionally tolerated sequence space for these stacked aromatic residues. Our findings demonstrate that the functional landscape of the interfacial aromatic residues within the Rad51 filament is highly constrained. In contrast, the amino acids at the equivalent positions within the Dmc1 filament exhibit a broad functional landscape. This work helps highlight the distinct evolutionary trajectories of these two eukaryotic recombinases, which may have contributed to their functional and mechanistic divergence.AUTHOR SUMMARYMost eukaryotic organisms have two closely related proteins, Rad51 and Dmc1, that are needed for different aspects of genetic recombination. These proteins may have evolved from a single gene that was duplicated during the early evolution of eukaryotes. Rad51 is active during both normal cell division (mitosis) and sexual reproduction (meiosis), while Dmc1 is only active during meiosis. To better understand how these proteins are related, we studied their three-dimensional structures using high resolution cryogenic electron microscopy. Our findings show that Rad51 has a specific set of conserved amino acids located at the protein interfaces, but this set of amino acids is different in Dmc1. We used a series of genetic approaches to analyze how these amino acids affect the proteins’ function. Our results show that Rad51 has a strict set of rules governing the identify of these amino acids, whereas Dmc1 does not. This research sheds light on how Rad51 and Dmc1 have evolved differently, leading to distinct functions in genetic recombination.
Structure of the SMYD2-PARP1 Complex Reveals Both Productive and Allosteric Modes of Peptide Binding
Authors: Zhang Yingxue , Alshammari Eid , Sobota Jacob , Spellmon Nicolas , Perry Emerson , Cao Tianxin , Mugunamalwaththa Thamarahansi , Smith Sheila , Brunzelle Joseph , Wu Gensheng , Stemmler Timothy , Jin Jianping , Li Chunying , Yang Zhe 
Published: December 2024

AbstractAllosteric regulation allows proteins to dynamically respond to environmental cues by modulating activity at sites away from the catalytic center. Despite its importance, the SET-domain protein lysine methyltransferase superfamily has been understudied. Here, we present four crystal structures of SMYD2, a unique family member with a MYND domain. Our findings reveal a novel allosteric binding site with high conformational plasticity and promiscuity, capable of binding peptides, proteins, PEG, and small molecules. This site exhibits positive cooperativity with substrate binding, influencing catalytic activity. Mutations here significantly alter substrate affinity, changing the enzyme’s kinetic profile. Specificity studies show interaction with PARP1 but not histones, suggesting targeted regulation. Interestingly, this site’s function remains unaffected by active site changes, indicating unidirectional mechanisms. Our discovery provides novel insights into SMYD2’s biochemical regulation and lays the foundation for broader research on allosteric control in lysine methyltransferases. Given SMYD2’s role in various cancers, this work opens exciting avenues for designing specific allosteric inhibitors with reduced off-target effects.
Development and clinical application of a methylated ctDNA assay in the preoperative risk classification of resectable colon cancer
Authors: Raunkilde L , Andersen RF , Timm S , Jørgensen M , Lindebjerg J , Rafaelsen SR , Hansen TF , Jensen LH 
Published: December 2024

AbstractBackgroundPathological lymph node involvement (pN+) is an indicator of poor prognosis in localized colon cancer. Currently, the preoperative risk classification fails to accurately identify pN+, which could be instrumental in the selection of patients for neoadjuvant chemotherapy (NAC). This study aimed to develop an assay for preoperative methylated circulating tumor DNA (meth-ctDNA) as a predictive marker of pN+ and as a biomarker for initiating NAC in patients with localized colon cancer.Materials and methods203 patients operated for colon cancer stage I-III at Vejle Hospital were randomly assigned (1:1) to a discovery and a validation cohort. A multiplex assay of a tumor-specific (NPY) and two organ-specific (GAL3ST3, KANK1) meth-ctDNAs was designed and methylation analysis was performed using droplet digital PCR. The ability of preoperative meth-ctDNA to predict pN+ was assessed using receiver operating characteristics (ROC) analysis.ResultsROC analyses of meth-ctDNA (negative/positive) to predict pN+ had an area under the curve of 52% and 57% in the discovery and validation cohort, respectively. Survival analysis in the validation cohort confirmed a higher rate of 48 months disease-free survival in meth-ctDNA negative compared to positive patients (HR=2.31, 95% CI 1.01-5.2). The difference also applied to 4-year overall survival (HR=3.62, 95% CI 1.15-11.4). In a multivariate analysis, meth-ctDNA remained the strongest prognostic factor of DFS (HR 2.46, 95% CI 1.03-5.88) and OS (HR 4.54, 95% CI 1.32-15.6) in relation to clinical T- or N-category, gender and age.ConclusionThe preoperative meth-ctDNA multiplex assay did not predict pN+. The findings suggest meth-ctDNA as a more powerful marker than N-category in identifying high-risk patients who would potentially benefit from NAC.